Nineteen years of
notes from the bench.

Starlyte Nebula Driver FAQ

TL:DR Live Debugging Get a Full list of Supported Drivers Testing a Specific Driver File Testing Host and Sub Devices Live Debugging Due to the open nature of our driver system, it’s relatively straightforward to write a new driver file…

Understanding TTL control, Blanking & Device Streaming, and why it matters for your research.

While this is an old subject in terms of technology, I find that every few years I end up describing it to a new group. Surprisingly to me, every time people seem to appreciate the information, and I think it’s just not covered often in…

Starlyte Nebula Now Supports Opto Gmbh Microsocpes

Thomas Spieker from Opto Gmbh was kind enough to send us a demo assembly of several microscopes made by his company. Opto manufactures a series of highly integrated microscope modules, all provided in a small, integrated form factor. I was…

Touptek Cameras Supported in Nebula

Recently, I had two different requests to support the cameras manufactured by Touptek. Ash from Scientific Imaging was kind enough to let me borrow one for in-house integration and testing. These cameras support Sony IMX-174 sensors, use a…

Allied Vision Cameras Now Supported in Nebula

Starlyte Imaging has completed support for Allied Vision array scan cameras. The driver suite fully supports: This addition enables users with existing cameras to easily integrate Nebula on machines used for inspection, materials…

Triggerscope Mini Micro-Manager Setup

Below is a short video introducing the Triggerscope Mini, as well as demonstrating how to set it up in micromanager. If you’re in a hurry, I’ve also outlined the basic steps below with screen shots. Connect the triggerscope mini to a USB-2…

Design of a cemented doublet lens using AI

How well can modern AI agents produce engineering designs for optics? Well – I wanted to find out. To test this, I’ll walk through my goal. I need to get a lens made and I need it fast. I also need it to work properly. Lastly, I need it to…

xTool Conversion utilities

We are about to announce some new products made using the amazing xTool UV laser engraver. Along te way, we needed to convert the 3d files used on the system to SVG. I figured I may as well share that, and so you can find it on my github…

Triggerscope Mini Released

Compact, Simplified TTL and DAC – Micromanager Native I’m happy to share a new device I’ve been working on after encouragement from numerous clients. This new smaller version of the Triggerscope is intended to bridge the gap between large…

Starlyte Nebula Adds Drag+Drop Merge Captures

Tool simplifies manual capture We had a recent customer asking to solve a rather standard but annoying problem. If I have a manual filter turret, and still want to overlay images, how easy is it to do? To solve this, we added the ability…

Starlyte Nebula Now Supports Excelitas LED Illuminators

Over the past few weeks, we’ve been building out driver support for the Excelitas illuminator line. Today i wrapped the Tetrem unit up. Below is a 2 channel illumination sequence using the Excelitas Tetrem, captured via a Hamamatsu Fusion…

Tucsen High QE Libra CMOS Announced

High QE, small pixel size Recently Tucsen had a presentation on their new Libra CMOS cameras which includes some nice improvements in sensor performance. Key highlights were: In a recent presentation here a series of improvements were…

Starlyte Nebula – Open Microscopy Control Software

A few months back, I started promoting a new software application called Nebula. As I introduced it to people I realized that I’d not explained the development or release of it on my website, and so here I’ll take a minute to explain that…

Nikon Ti-E EPI Filter Wheel

What to look for and how to replace the drive gear The Venerable Nikon Ti-E remains in service in research labs all over the world. One of the first autofocus-enabled instruments deployed with the integrated PFS, there isn’t much to ask…

Why a $3 laser vs $5000?

I made a short video describing why laser pricing is so different. Much of it comes down to how precise the beam performance needs to be, and as with so many similar fields, as precision becomes better and better, pricing begins to log…

Firmware setup for Micromanager

Here is a quick video on how to get going with the TriggerscopeMM Firmware and Micromanager 2.0 Gamma. -Austin

Triggerscope Driver Available for Volocity

ARC now has a driver available for users of Quorum Volocity microscopy software. New releases of Volocity will include native support. If you need a driver file or assistance please contact ARC for support. -Austin

Zaber MVR Automated Invert Review

By: Austin Blanco & Garrett Bunch One of the toughest aspects of working as a consultant engineer is that the coolest and most interesting projects are the ones I don’t get to talk about or share online! But as time marches on, sometimes I…

Setting Triggerscope Range Values

Here is a quick example of using the RANGE controls in the Triggerscope GUI Application, as well as an example of saving ranges to the on board SD Card. EDIT – Fixed Video link!

Triggerscope 4 Getting Started Video & MM Firmware

We’ve made a new video example of how to get things set up on the Triggerscope with the “Micromanager” version firmware from Nico. Please take a look if you are interested in updating your Triggerscope to use this code, or if you want to…

New Product Announcement – 3.3 – 5V TTL Level Shifter

Recently one of my clients was working with a Blackfly S camera from FLIR, and noticed that the TTL signaling was not working properly. With some investigation, we discovered the cause to be the camera running at 3.3V output TTL, with very…

Triggerscope 4 Released – with New Software and New Micromanager Driver Options

I’m excited today to announce the release of the Triggerscope version 4. TG4 marks a major improvement in the performance and capability of the Triggerscope. New Features New Software In addition to the release of Triggerscope 4, ARC is…

Raspberry Pi High Quality Camera – Can it be Cooled?

Thanks to some generous industry friends, I finally managed to get my hands on a seemingly unobtanium RPI “High Quality” camera. I’ll have more info on the camera itself regarding performance, but my first question was – “can it be…

How to Succeed at Working From Home

All over the world people are being asked to work from home… Yet how many of us have had to do so for extended periods of time? As a case in point, are you reading this now while sitting at the office? Or, worse – while sitting at home…

8020 Extrusion Optic Sliders

For some time now I’ve been using 8020 extrusion for quick prototyping of optical assemblies. It’s great for assemblies which require longer focal lengths and larger elements. For such systems, the choices are to use a breadboard or table…

Laser Alignment for Microscopes Using 3D Printed Parts

A few months back I was working on a custom microscope that required several sections to be aligned. The camera to be centered on it’s axis and aligned to the objective, the excitation wide-field illuminator to be aligned to the back…

High Speed Triggering for Micromanager using Triggerscope Stream Script

Over the past few years, I’ve often battled the Micromanager MDA window, when needing to perform high speed triggered acquisitions. While the system works well for multi channel Z stacks, running timelapse 2 channel streams, or “Z first”…

THOR SM1 Threads in Fusion360

I frequently build parts, both aluminum and 3d printed, which are used with thor components. Using Fusion360 from Autodesk, it’s simple to add threads into a hole, or even create pre-threaded holes in objects. Luckily, Fusion360 even…

Lab Automation using Arduino

This is a great example of using Arduino in the lab. If you have limitations to your Lab hardware, and want to explore how to expand or modify it, please get in touch, as this is what we do! -Austin

On a lifetime of Learning

Like so many who live in the sciences, I am fascinated by all things new, unknown, or barely discovered. I think some people just have this innate sense of a continued drive to understand, to improve our awareness and knowledge in the…

Setup Guide for Triggerscope 3B Using MicroManager

Required Components and Preparation For a new Triggerscope 3B shipment, remove from packaging and account for the following: Hardware Connections Once unpackaged and all components are accounted for, plug the 12V power supply into the slot…

ARC Expands Technical Talent

As client demand continues to grow , ARC has been looking to expand the team, and is pleased to announce the hiring of ARC’s first employee, Daymian Rocca. Daymian joined the team as Technical Systems Engineer Jan 15th, and brings to the…

New Triggerscope 3-B Adds Range Spanning, LEDs, High Current Drive and More

I’m excited to announce the release of the newest Triggerscope model the 3-B. This version replaces the V3, and is packed with improvements for practical laboratory use, including: DAC Software Range Selection Range selection is now…

Live Animal Imaging Confocal Activates Vascular Clotting

On a recent project I had an opportunity to collaborate with some great manufacturers and vendors, to build a custom microscope for Dr. Chia-Yi (Alex) Kuan, at the University of Virginia School of Medicine. This instrument is quite unique…

Vortex mixer mod using Ryobi Orbital Sander

During a recent project for a client, I had to prepare a fluorescent bead slide for imaging. Beads require dilution, and a vortex mixer is recommended in order to provide ample separation of the individual beads. Not having one on hand, I…

Polarization sensitive cameras for Microscopy

Flir is pushing these new Sony sensors, along with Lucid, for use in remote sensing and inspection. These are interesting. Basically each camera can capture 4 polarization states in one image. I can imagine these may be used for several…

Mac OSX Serial Terminal for ARC

I’ve long wanted to build a terminal and testing application for my products. Using the exceptional QT Creator, I was able to cook one up in a relatively short period of time! This application was built using the QT Terminal example…

ARCLED 8 Channel LED Engine

I’m happy to announce a new product made by ARC. Over the years I’ve worked with a large number of illuminators, from mercury excitation lamps to laser combiners. I’ve tried to combine the best traits of a light source into this device…

sUAS Drone Pilot Test Resources

The resources below are for students attending my drone courses at Norcal Flight Center, but if other readers stop by, I hope you find these useful! The FAA classifies certification for commercial use of drones as an “sUAS” cert. Or, a…

Looking for Alzheimer’s in the Eye

I’m excited to share the following publication from my colleagues at Neurovision Imaging & Cedars Sinai Medical Center. This paper represents a ton of work, from people all over the world. I’m also happy to say I had a chance to play a…

Sine wave Generator from iPhone

I keep looking into a low cost, yet stable way to generate nice sine waves which are controllable, using something other than a signal generator or one of the cheap breakouts which never seem to work that well. This led me to considering…

New Site Design

So i finally spent some money on a decent site theme. I hope you like it! If anyone experiences any issues in using the site with this theme, please let me know! -Austin

DIY Syringe Pump

Interesting little project. Not sure the money pans out considering how much time it would take to build, but if one wanted to learn mechanical control, this would be a good way to dive in! https://www.drdflo.com/syringe

Cooling a Pt Grey Camera

I’ve been working with Pt Grey (now FLIR) cameras for a few years now, and one nagging question in the back of my mind has been whether or not it is possible to cool them via external means. There are basically 3 categories of cooling when…

Calling all Arduino and Raspberry Pi Users!

Do you build systems which use Arduino or Raspberry Pi boards? Are you happy with the enclosure options available today? I’m not either. But I’m having some trouble figuring out the best possible products to offer. So, I figure there’s no…

LED, laser, or other PWM control using Triggerscope

It appears that more and more people want to use PWM control for illumination devices from Micro-Manager and other imaging software. PWM may be used for any number of applications, from high speed pulsing of an LED, or a laser, in order to…

Intel NUC, Pt Grey camera and ASI RAMM offer serious performance for a great price

One of my recent projects which was very exciting and interesting was to build a custom imaging system for John Mclaughlin at Torch Therapeutics. This was a great build for a number of reasons, one of which is that Torch has allowed me to…

Micro-Manager on the Raspberry Pi

Micro-manager guru Kyle M. Douglass recently posed his implementation of micro-manager on a raspberry Pi 3. Very cool potential here, considering when the computing power of the pi is exceeded for a given application, one could just add…

Computational imaging continues to grow in microscopy

The Waller Lab recently had a demo announcement of their awesome implementation of computational imaging. They have some examples on their lytro page, which look really cool! This got me thinking about the last 10 years or so, and how the…

An awesome gerber viewer for OSX

While there are a few viewing tools available for OSX, I’ve been looking for something that was higher quality, and more configurable. Today I stumbled upon Cuprum. This viewer supports layering, export of user-configured views, some good…

Largest Image of the sky ever taken

The Pan-STARRS observatory released this single image of the entire night sky, in late Dec. Amazing! An 11MB download is available here. Reference – http://www.ifa.hawaii.edu/info/press-releases/panstarrs_release/ -Austin

Black Friday / Cyber Monday Discounts for Builders & Makers

Hackaday has a great list of links on whats available for black Friday & Cyber Monday. I found this a great deal – Autodesk has an offer for 2 years of Fusion360 for only $60/yr! My local 3D printer manufacturer, Printrbot, has a 10% off…

Pt Grey Camera Driver for MicroManager unleashes low-cost microscopy

Let’s say you want to build an imaging system, but you want to attach 2 cameras for time-correlated 2 channel imaging. The limiting factor for such an arrangement is usually cost, that cost being $10,000 USD per camera means $20,000 for…

Data Logging in the Cloud

I’ve been working on a project which requires data logging from a mobile device over several days. I came across a neat site which supports simple uploading and view/export of data, from numerous sources. It’s called thingspeak.com. Once…

High speed stable enclosure for GoPro and Black Magic cameras

Here’s a project I can finally talk about! This is one of my clients, PEOVI, who makes rugged, high speed camera mounts for anything from race cars, to airplanes. If you need to mount a Black Magic Micro, or GoPro, to your high speed…

95% QE SCMOS vs. EMCCD

In 2011, I reviewed the Andor Neo, one of the first scmos cameras commercially available. I ended my report with this statement, “…there is much life left in the good old frame transfer sensor…until someone cooks up a back thinned scmos…”…

Microscope Objective Zemax Files

While I haven’t had a chance to test these for accuracy, I was excited to find them while looking for some tube lens specs! You can find the file set here. These designs include some of the common infinity corrected objectives, as well as…

Shutter Configuration of TTL devices in Micromanager

I made this video to show how to use both a state device shutter object and a group shutter object in micro-manager. Hopefully others can make use of it!

Build a Stratux in 10 minutes! (ADS-B)

As the 2020 FAA mandate for ADS-B comes upon us, more aircraft are using the ADS-B system. Additionally, weather transmission via towers is a major free source of in-flight weather info. Having recently picked up a new iPad, and…

Dynamic Mirror Reflection Angles using Fusion360

SO I’ve been working with AutoDesk’s Fusion360 for a while now, and have found it to be an exceptional tool for diving into CAD. If you’ve considered CAD before, but have been scared off by the learning curve, I recommend checking it out…

Optical Design comes to the iPad!

Over the past 5 years, almost every project I’ve worked on has required some level of optic design. In many cases, simple designs suffice. For example, projecting an LED can be accomplished at a basic level with an aspheric condenser. But…

Automated Capture and Save script for Micro-Manager

I wrote this for a client, but figured others could make use of it. This code simply captures a number of images as defined by the user, and saves them to the specified folder without displaying them. This is useful if you don’t want all…

A serial monitor that works in Win7x64!

David Biggs at KB Imaging LLC put me onto this serial monitoring software, called SUDT Accessport . I’ve used it a bit for some work on the triggerscope, and it works very well! You can watch data transmitted between USB emulated serial…

How to use external triggers on scientific and industrial cameras

Controlling a camera from an external trigger can be very useful. External triggering provides greater timing accuracy, direct control over exposure duration, and remote operation from TTL devices. This is a prime reason I made the…

DIY emission filter for observer safety

I can’t believe I missed this excellent post from Sam Lord @ Everyday Scientist on how to insert an emission filter on your ocular lightpath. Having been hit by some untold number scopes wherein I either was observing, and switched to a…

uPeek iPhone based Microscope

Kickstarter has another iphone microscope project, this time it looks like an attachment which includes a 4 line LED, focusing and optical element system, and machined body. Looks cool! -Austin

Merry Christmas!

Figured I’d post another SEM shot of a snowflake. These never cease to amaze!

Experimental FM transmitter using Raspberry Pi 2

If you have an extra Raspberry pi around and want to try something fun, you can use the GPIO on the pi to transmit at FM frequencies. For the rPi v1 you can use this link for instructions. For Raspberry Pi2 I found a great application…

Site Updated!

What do you think of the new site layout? I was looking for a simple, clean interface that works well on conventional and mobile browsers. Hopefully, I’ve found it. If anyone has recommendations, please feel free to comment!

ASCB 2015 Reveals the Next Generation of Microscopy

One of the best aspects of flying is being apart from the world. Not only terra firma, but the troubles of life, questions of the future, and concerns of the present. Flight requires attention to instruments while in operation, but long…

iPhone 6s Zoom & Resolution

Ever notice that no matter what zoom setting you use on an iPhone, the resolution of the captured image is the same? This defies convention, as normally, as a sensor is cropped digitally, the resolution of the resulting image should…

Triggerscope & Micro-Manager Demo LED

With ASCB right around the corner, I’ve been looking for opportunities to showcase the controller, so I’m happy and grateful to announce that the TriggerScope16 will be demonstrated at the Open-Imaging Micro-Manager booth (#1312) this…

RGB to Wavelength Converter

This is a useful tool I found while getting ready for ASCB. Hope others find it useful! http://academo.org/demos/wavelength-to-colour-relationship/

TriggerScope2 and TriggerScope16 Released

I’m excited to announce 2 new products from Advanced Research Consulting. The first is a new, 16-Channel, 16-Bit DAC controller. This controller uses a high accuracy multi-line DAC IC to provide more DAC lines than any other product…

Cutting Filters using a CNC

SO I had a project where I needed a specific size of beamsplitter and I needed it quickly. Unfortunately, the type I needed wasn’t available from the usual sources, at least, not without a few days of lead time. What to do? It turns out…

High Speed Microscope Automation using stand-off controllers

In my previous post, I reviewed the current performance of available microscope control applications like Metamorph, NIS Elements, and Micro-Manager. Of course, using the Metamorph software device streaming function produced a hands-down…

Acquisition Speed Comparison of MetaMorph, NIS Elements, Micro-Manager

How fast can a typical imaging system really run? What factors affect this? While most research might not require rapid sequential capture, almost all experiments can benefiet from tight exposure/illumination timing, yet few microscope…

Sub $2 microcontroller solution

I’ve been working with Arduino boards a lot lately, and they are great. But some elements of the arduino can be even better. What is an Arduino? An Arduino is a breakout board for the Atmel “ATMega” series of microcontrollers. These…

Echo Laboratories launches the Revolve Microscope

Over 450 years have seen the compound microscope evolve into an incredible instrument. From simple contrast viewing, we’ve moved to super resolution systems capable of sub-diffraction accuracy. But for all this advancement, we’ve been…

Countdown to a Revolution in Microscopy – Day 1

Well, I guess I should continue providing lengthy explanations of this skunk works project, but I think it’s time to let this thing stand on it’s own merit. So…here’s a nifty countdown timer until the announcement goes up! The wait is over…

Countdown to a Revolution in Microscopy – Day 2

I was supposed to write about bigger/faster/stronger today, but I don’t want to. Instead I want to consider culture. Companies absolutely have cultures, or rather, micro-cultures. Labs have cultures as well! One can consider in many ways a…

Countdown to a Revolution in Microscopy – Day 3

Every so often I will get the chance to cook up some code for one of the usual software scope control packages. But these days, I spend most of my time in programs like Fusion360, Fritzing, and the like. So I guess this is how I feel when…

Countdown to a Revolution in Microscopy – Day 4

What can’t your microscope do? Any user of a modern scope, or at least, a high end scope, considers the addition of new widgets. Whether it’s a better illuminator, adding a more sensitive camera, or even a motorized component, we think of…

Countdown to a Revolution in Microscopy – Day 5

The foundational design of the compound microscope has, in many ways, remained locked in place for the 450 years of it’s existence. Combining an objective, eyepiece, and illuminator to provide a magnified view of a specimen has drastically…

iBiology Microscopy Courses

Here are some exceptional videos covering a soup-to-nuts overview of modern microscopy, techniques, and applications. iBiology Microscopy Full Course iBiology Microscopy Short Course

Op Amp Design Reference

I came across this excellent design reference, which shows quite a few basic op amp design examples. Great guide to keep handy should you be working on amps! Op Amps For Everyone

Running HASP Licenses on Virtual machines

One of the downsides to using OSX for my primary operating system is that most of the major imaging programs are windows-only. To compound the trouble, many of these programs, like NIS Elements, use the “HASP” license manager to…

Arduino Mega 2560 Comparator

So I needed to set up an Arduino Mega as a signal processor. I had a sawtooth signal coming from a device, and I wanted to convert that signal to a 0/5V TTL signal. Now, with something like a sine or sawtooth wave, the question becomes…

Identifying Astigmatism in your microscope

After all of the engineering and testing which goes into a microscope, you’d imagine that any manufactured scope would have perfect alignment of the optics. Believe it or not, in many cases things can be off! So how can you tell this? A…

MetaMorph, Elements, Micro-Manager intermittent Crashes may be due to power options

Does your system crash when taking a timelapse, or just every so often, but isn’t linked to a specific set of actions you take? Or, does your camera run slowly for no apparent reason, only sometimes? Here’s a basic set of checks to do…

Is there anything cooler than drilling gigantic holes in the ground? Yes – Blowing stuff up afterwards!!!

I’m sure this study involved no fun whatsoever 🙂 http://www.nature.com/nature/journal/v518/n7537/full/nature14146.html -Austin

Wide-field, high-resolution Fourier ptychographic microscopy end runs conventional limits to resolution

Dane Maxfield from Technical Instruments send me this interesting article from Nature. It’s great to see the power of image processing be used in such a way, and my guess is that this type of image+software+hardware combination will yield…

Nikon Immersion Oil Comparison

Sam Lord at EveryDay Scientist has an excellent review of the available immersion oils for microscopy. Check it out here! -Austin

Into the Wild….

I’ve had an actual “job” since I was 15. Of course, my first work was mowing lawns as a kid, moving firewood, cleaning up rental houses, the usual “make a few bucks” stuff. When I was 15 I had a chance to become a beta tester for a book…

The TriggerScope Controller

I’m happy to announce a new product for microscopy, the “TriggerScope” controller system. I hope this device will prove itself useful in many areas of microscopy, but the basic idea is that it can drive scope components via manual control…

Voltage Dividers

Happy New Year! I’ve been experimenting with a simple way of pulling a single power source into two rails, ad the simple solution is to use a voltage divider. One of the best explanations I’ve found on how these work is this excellent…

Adobe Brackets is a nice, free text editor

I recently was working on some file transfers using filezilla, when I needed to edit a php file. Filezilla has a “view/edit” option, so I clicked it figuring, “ah, this likely won’t work, but I’ll give it a try”. To my surprize, it…

NA vs. magnification, or why a 60x objective is brighter than a 100x

Microscope objectives are typically classified as being brighter or darker based on NA, or Numerical Aperture. This is for good reason, as the NA of a lens will affect both the amount of light delivered to a specimen (excitation) and the…

More on CMOS Rolling Shutter

A friend sent me an awesome and interesting article on petapixel with some excellent examples of how rolling shutters work on cmos cameras. (Thanks Hoy!) This is directly applicable to scientific CMOS cameras, IF you are using the “rolling…

Useful tools (and where to get them)

PopMech has a little blurb on good cheap useful tools here But I’d add that the best place to find such tools is Harbor Freight. Now don’t get me wrong, I’ve found items like cutting tools, abrasive pads and the like to be of marginal…

Aviation – the invisible highway

Looks like a great documentary – then again, I’m biased towards all things aviation 🙂 Aviation: The Invisible Highway (Trailer #1) from Aviation: The Invisible Highway on Vimeo.

Long term considerations when building or buying an Imaging System

Years ago I worked for a major imaging camera supplier. During one meeting with a team of engineers, we were discussing some really cool aspects of a camera and driver suite for that camera. The engineers were showing us “kinetic…

10 Years of Cassini’s Look at Saturn

Some beautiful pictures of Saturn here. As a child my great uncle Dan, who worked on the fuel mixture system for the STS series shuttle, showed me saturn through a small telescope. I will never forget looking at those rings, and my wonder…

Rail to Rail +5 / -5 Power Supply from USB

When working with amplifiers, it’s crucial to keep as much noise out of your power supply as possible. Most of the time, your power noise will end up being amplified or will at least show up in your resulting signal as pattern background…

Hilarious Correlation examples

I’ve always loved the “global warming vs. piracy” graph, but this is a whole new level of funny. Click the pic for more examples! -Austin

Metamorph MetaMobile App provides remote view and control of your scope from an iDevice

I was talking with a long time friend from the MetaMorph team and was surprised to learn they have had an app-based control package available! I haven’t tried it yet, but the next time I get my hands on a meta-controlled rig I’m definitely…

Airbus E-Fan is a step in the right direction for GA Electric Airplanes

Just saw this video from Airbus, which shows off a ducted fan electric training plane. Personally, I’m wondering what happened to the Electric Cessna 172 project from a few years back. That project was bought and then went dark…

Due Diligence for the average News Reader

This is a great explanation of why most news regarding evil dangerous “chemicals” or miracle substances are half-baked. I wish they’d play this as a PSA on evening broadcast TV instead of the usual stuff… A great example of the whole…

Tetris at the Philadelphia Cira Centre

I’ve always enjoyed a good tetris battle, so watching this made me think of what could be done on a series of buildings…

Arduino Timer Libraries

Found these great timer libraries for a far greater level of control over Arduino PWM functionality. Very cool! TimerOne & TimerThree Libraries by PJRC

2014 Lunar Eclipse From the Pacific Coast

This monday I had a chance to take a few shots of the moon as we caused an eclipse. You can see a bit of the “blood moon” effect as well. The shooting conditions were OK, high altitude stratus obscured the view, but it was viewable! My…

Perfect example of a Conference Call

I think everything shown here happens on every conference call I’ve ever been on!

Tonight marks first “Blood Moon” lunar eclipse

For those on the west coast USA, this will begin just before 10PM, and conditions should be perfect (clear skies, dark, early enough to watch and not miss sleep!) – I’ll take pics and post what I get!

Bureaucracy vs. Harm – is science suffocated?

A new website observes that today’s scientific research is hindered by excessive regulation and oversight. On a spectrum of two possibilities, total anarchy in research vs. total control, where do we stand? I’d guess it depends on what…

Airpooler is the Uber of the Air

Ever since using services like AirBnB and Uber, I’ve been thinking of a system which would provide ride shares for pilots. Almost every certified airplane has 4 seats, but most flights are single pilot operations. Meanwhile, there are…

Low Pass Filter for PWM to DC

I’ve been working on a project where I needed a consistent DAC signal to be sent from a control device to a sensor. The sensor wanted a voltage input which was steady, but arduino boards don’t have true DAC output, rather they use PWM to…

Reading Rotary Encoders with an Arduino

The Arduino IDE for ARM microcontrollers is just plain awesome. I’ve been using both an Uno and a Mega board for quite a while now, and continue to be impressed with how flexible these inexpensive boards are. Recently, I wanted to read the…

10 Actual Mad Scientists

I’ve heard of a few of these, but this is a great list!

Tethering an SLR to Micro-Manager

Just a heads up if you plan on using the NK Remote tethering solution for Micro-Manager. It appears as of now this solution only works in 32 bit installations of windows. I believe a great alternative would be to figure out a driver…

Open Cellular Protocols Pave Way for Development

I was just thinking about this issue on my morning walk. So my wife and I travel to Mendocino, and there’s no cell coverage. On one hand, it’s kind of nice to be disconnected, but on the other hand, I’m thinking, if some entrepreneurial…

Will this Entanglement Experiment solve the Ultimate Question?

This is an interesting proposal to deal with the “watchers causing a change” phenomenon in quantum mechanics. Of course, answering this would answer the question of “free will”. Crazy! There’s a funny, and interesting youtube video on this…

Will Pelican Imaging change photography forever?

I think this type of hyper-focal imaging tech will bring as yet unimagined possibilities into photography. Remember when the idea of a Digital SLR was ridiculous, because CCD’s didn’t have the dynamic range or resolution to compete with…

Growing up in a Maker World

Reading this article about Brook Drumm, fellow Lincolnite and 3-D printing champion, brought to mind my journey of building, and breaking, everything I could get my hands on. I remember many years back when I was 10 years old, I had a…

Top 10 Lowest Flybys?

A friend sent this and…well…this is just an awesome use of military hardware 🙂

3-D Printing – Reality vs. Advertising

About a year ago I backed a Kickstarter project for a 3-D printer. A few months after some typical Kickstarter delays (production trouble – etc), I received my shiny new printer in a big box. After setting it up I realized one thing: I had…

A year of Kickstarter

Having backed a few projects this year, I really enjoyed this short presentation. Kickstarter is Awesome!

Hiding text inside images

This is an interesting way to use image processing. It’s a program which encodes text into an image or into a sound file. Looks like something for the spy world but it’s something I never considered for image processing. Cool stuff!

The EyeCam, or What I’ve been up to the past 12 months…

So over the past year I’ve been working on a product which I can finally talk about. It’s a retinal imager which uses the iPhone 5/5S as a capture/storage system. For now the only specs I can give is that the images are wide field, and…

Arduino Controllers – Flexible low cost programmable control systems

I’ve had a chance to play with an Arduino Uno for the last few weeks. It’s a really neat programmable controller. So what is an Arduino, and why would anyone want to play with one? In short, an Arduino can be thought of as a…

Storing your data – Cloud vs. Local Storage for Imaging Systems

Anyone working in imaging knows that one major ongoing problem is handling the massive amounts of data collected. A relatively low resolution camera can output massive volumes of data, if combined with a stage, z motor, wavelength…

Organic CMOS sensors provide enhanced dynamic range and larger fill

Fujifilm and Panasonic have announced development of an “organic” photoelectric conversion layer in place of a traditional silicon photodiode used in conventional systems. Obviously it will take a while for this technology to trickle into…

Field Microscope for $150

This is a cool attachment for the iPhone. An optical system that produces 20X-80x image magnification, and has a contained adjustable illumination source. This is an interesting product, as it will by no means replace a stereo scope for…

The journey of rebuilding an Airplane Engine

Back in mid December I had the unpleasant experience of a large bird flying through my prop. In the aftermath of this event I learned that my engine had to be inspected internally, to determine whether any internal components were damaged…

The End of EMCCD is Near

Canon is showing off a new CMOS sensor which it won’t really explain, but it compares the sensor to an EMCCD (3 chip) camera. The differences are amazing for color acquisition. Once this tech becomes quanitatively measureable, it will…

Why Every iPhone Owner (especially Pilots) should buy an OlloClip

I’ve been using an Ollo Clip for a few weeks now, and it’s a well established, very cool product for the iPhone. I’ve been using the 4S version, and the 5 version was also recently released. So – why buy an OlloClip? The iPhone camera…

An Interview with Nico Stuurman of the Micro-Manager Project

Having worked with Micro-Manager for the past several years, I’ve been intrigued by the progress and impact this open-source software platform has had in the life science imaging community. Micro-Manager is changing the way we think of…

Switch LED Light Bulbs Released to Market

Quite a while ago, I posted on the super cool (literally and figuratively) Switch LED light bulb. These bulbs promised the holy grail: color quality, low operation temp via efficient cooling, and high power. Today I received news they have…

Lasers used as a Tractor Beam?

For years lasers have been used as tweezers, but this is a new approach to using a laser as an attractive force. In a paper titled, “Experimental demonstration of optical transport, sorting and self-arrangement using a ‘tractor beam’”, the…

Nanometer focus and positioning

Interesting methods described in this paper from Stanford. As super resolution systems gain popularity, problems like this will become more apparent, so this has perfect timing… -Austin

Rolling vs. Global Shutter modes in CMOS cameras

There’s a good article explaining the difference between these exposure modes here – http://alliedscientificpro.com/rolling-shutter-or-global-shutter-modes-for-cmos-cameras/?goback=.gde_1628247_member_202082300 Bottom line for any…

Collimating LED light

Nice article on how to collimate current high power LED sources, and why it’s needed. http://lightguide.blogspot.com/

Simple Low Cost Laser Power Meter / High Speed Light Sensor

If you need a low accuracy qualitative power meter, for either standard or laser light, or if you need to sample a light source for it’s speed/frequency, you can do so using a $5 electronic component called a phototransistor. Basically a…

Characterising unknown optical components

Whether you tinker with optical components or professionally use them, sooner or later you’ll come across a optical component that isn’t marked. So, rather than toss it, can you find out what it’s performance and properties are? Yes and no…

Playing with the Speed of Light

MIT is releasing a game and new engine which allows the player to experience the effects of changes to the speed of light. Very cool way to show these effects!

Getting the most from Fiji on your Mac

Fiji is an excellent fork of imageJ, but one limitation of the build is that many of the plugins used with it are compiled only to run in x32 environments. If you are running a modern Mac, you may have noticed that the status bar in the…

Ghosts of WW2

There is an amazing collection of images on flicker by Jo Hedwig Teeuwisse which uses original WW2 photos and newly shot photos from the same locations in several cities in Europe. Very interesting application for image processing, and…

Next Steps for Quantum Computing?

Interesting research on realizing a quantum system. Hope it works! -Austin

Using a Virtual Machine to Expand your computer’s capability

In my recent job change I was asked what type of computer I wanted for daily work. I could choose a desktop or a laptop, either Mac or PC. I’ve been a PC user since before DOS, in fact my very first computer was a TRS-80 on which I learned…

Last flight of the Space Shuttle and the end of an era

Last Friday I was privileged to watch the Endeavor fly over downtown Sacramento, CA. The Endeavor was atop it’s transport 747 as it made low passes over several cities in California. Watching it fly over reminded me of being a child…

ImageJ 2 Almost released?

I had a chance to check up on the ImageJ 2 project. The version 2.02 beta was released a few days ago and I played with it a bit. There are a lot of things left to be done for sure, but it looks like the project is coming along well. You…

Nikon LU4A Fiber hack

Many people who own a Nikon C2 or A1 confocal may not realize it, but the laser launch used with these confocals may include an optional second fiber output. The LU4-A version of Nikon’s laser launch includes a 2 fiber option for systems…

$35 Spectromoeter Project on Kickstarter

Cool project for easy build of a spectrometer. This group already has the software available for download here, and you can see a how to on building a spectrograph from available parts here. If I get a chance to try this out I’ll post a…

Everything changes….

Five years ago I moved back near my hometown in California, to take a local imaging sales job for Technical Instruments covering UC Davis. Over those four years I had children, completely changed my job title and territory, and learned…

Hoverbike is here?

I’m guessing these are short videos due to the lack of a good power source. Still, very cool tech:

Some non-imaging fun

I haven’t been posting much as I’ve been on vacation a bit of last week. During my trip I was able to spend some time rock crawling in a friends Toyota Cruiser. This is a 40+ year old vehicle, that’s been so rebuilt and well maintained it…

OUYA is exploding on Kickstarter

As anyone who reads my blog know, I’m a big fan of Kickstarter. I was able to acquire the benefits of owning a CNC machine for about 1/10th the cost of a commercial system. I’ve also recently backed a dual extruder project, which just…

3-D Viewing Software for Biologists

I was looking for some data on common 3-D analysis techniques when I found this great resource from UNC Chapel Hill.They have programs for 3-D viewing, point tracking, and a few other interesting things. The ImageSurfer program looks…

Will SPIM kill the confocal?

I’ve been hearing more and more about SPIM systems, or “Light Sheet” microscopes. They rely on a simple change in the use of objectives, which provides one objective for excitation of an imaging plane, and another objective for collection…

250 Posts and counting….

Today I reached my 250th post. Interesting benchmark consider how it seems I’m never posting as much as I’d like. I guess I’ll have to make an orchestrated effort to hit 500 posts in 1/2 the time! Of course, to all of you who visit my site…

STORM comparison from UCSF NIC

I recently received a beautiful comparison image produced by the now operational STORM system at the UCSF NIC.The sample was prepared by Michael Davidson, and was imaged by Kurt Thorn of the NIC. Click the image for a higher res view…

ASI RAMM Microsocpe Testing

Over the past few years, ASI has cooked up a modular microscope. The design was for an optical bench that would support a wide range of configurations, as well as rapid adaptation and expansion. The system relies on conventional lenses…

Sutter Instruments TLED Transmitted LED Illuminator

Overview: Traditional transmitted lamps used on microscopes have several limitations. They don’t auto-shutter (turning off and on is rather slow, and requires the addition of a mechanical shutter for high speed multi-site acquisition)…

Top 5 Apps for Microscopy

Sorry to be away for so long! Still working on a special project which I will illuminate soon… In the meantime. I’ve collected up my favorite apps for microscopy: #1. Rescalc – I consider this #1 because of it’s immediate and useful…

Nanotechnology Progress

This is good news! Sorry posting’s been light. I’ve been working on a project which I will post about quite a bit in the coming weeks. But for now – it’s a secret 🙂 -Austin

Low cost open source Colorimeter / Spectrophotometer Project

This is a nice alternative to a $7,000 spectrophotometer. It’s also a lot smaller and hackable!

Coupling SIM and a Confocal?

Andrew York from the NIH has done this, and is reporting good results thus far. Interesting technique! I’m curious how the overall sensitivity of the instrument is, but the examples posted thus far look great! PDF – Google Code Site –…

2012 Annular Eclipse

Yesterday evening I was able to collect a timelapse series of the annular eclipse. My location was outside of the complete annulus, but it was quite close! Below is a quick youtube video of the timlapse as well as a few stills. I used a…

COMPLETE FLUORESCENCE FILTER LIST FOR MICROSCOPY

This post will grow over time, but I’m posting this so that researchers and vendors have access to one single repository of filter info. Hopefully this will make all of our lives easier! Definitions: ET – Chroma name for a sputter coated…

Posting’s Been Light

I must apologize for my lack of posts – I’ve been traveling a lot these past few weeks for work. In my travels I’ve come across this exceptional timelapse montage from Shawn Reeder. He spent two years putting the shots together. Timelapse…

HDR Microphotography

One of the most overlooked capabilities possessed by digital capture is what can be accomplished by image processing after capture. In modern EMCCD cameras, some processing is done directly in the camera head. Simple adjustments like…

Formulas for microscopy

I had a customer recently ask for these, and I thought I’d post them. These are from Nikon Inc. I’ll also have them on the resources page for reference. These include Useful magnification, Brightness Factor, Refractive Index, Depth of…

TRAINING DOCS FOR FIJI STANFORD COURSE TODAY

If you’re attending the training course on Fiji programming at Stanford, you can download the example files here.

Synergy Aircraft to offer Kickstarter Funding Round

Synergy Aircraft is making a push towards it’s next level of research in a composite blended wing/tail concept. They physics models show that the design should produce superior flight performance over several extremes of the envelope, i.e…

NIS Elements v4 and Bio Formats in Fiji/ImageJ

I’ve been receiving reports that images saved using NIS Elements V4 are not always opening under the typical plugins used for Fiji and/or Image J. If you plan on running a big set of acquisitions I recommend testing a few images before…

Confocal Microscopy Explained

Kurt did a great job on this comprehensive video which covers spinning disk and point scanning methods.

BIDC Seminar 5PM @ UCSF

I’ll be presenting today at the BIDC on “MacGyver Microscopy” at the UCSF Parnassus campus. Hope to see you there!

More from the UCSF 2012 Course – Last Day

Another excellent STORM image from the course:

STORM images on the last day of the UCSF Microscopy Course

We’ve been acquiring absolutely stunning data from the STORM rig at the course. Here’s an example! This is a 3-D image. The Gaussian spots indicate molecules which were detected.

The UCSF Microscopy Course Continues

A quick update from the course at UCSF. I shot this video at 9:30pm Tuesday night. Hard work for all but a lot of fun! Here is a video showing the Agilent MLC Laser Launch working on a Ti-E for TIRF, imaging beads. You’ll also see a white…

Some Pics from this weeks Microscopy Course

Studens and faculty alike have been working long hours at the inaugural UCSF microscopy course. Yesterday’s training covered ray theory to fluorescent imaging, and the students were running the last lab until about 8:45pm! Today will cover…

UCSF Microscopy Course – T minus 1 day

Most of our device manufacturer representatives have shown up at the course, along with piles of gear. This room was empty as of friday!

Into Space and Back in 400 Seconds

It’s a slow start, but the camera follows booster separation and return. Crazy video!

How to hack your imaging system

I’m presenting on “MacGyver Microscopy” at the BIDC on Thursday April 5. Please feel free to attend as the lecture is available to anyone interested! I’ll cover some fun topics like: – Home-Brew Device Triggering – Image Filters Used for…

Nikon DS-Ri1 Camera and Pixel Shifting on x64 NIS-F

Nikon officially supports Elements “F” (Freeware) on 32-Bit windows platforms only. While my colleagues and I have been able to employ x64 drivers and use NIS-F on Win7x64, the DS-Ri1 has been an exception. The Ri1 has a very specific…

Solar CME Produces amazing Light Show

UCSF’s NIC Youtube Feed

There are some great examples of imaging techniques here: http://www.youtube.com/user/NikonImagingCenter/feed -Austin

Is this the best startup launch video of all time?

This is absolutely hilarious – and a really good marketing technique:

Blogging has been light

I’ve been busy installing a new engine in my airplane this weekend, so I haven’t had much time to post on things, but here are a few items of note: Slides that use nano channels to produce super resolution images Just two weeks until…

Nikon nSIM wins #5 in TheScientist’s 2011 Best and Brightest

Here’s a short video review of the top 10 innovations in 2011. Some really cool technology here! Top 10 Innovations of 2011 from thescientistllc on Vimeo.

ImageJ Counting Macro for Known Field Values

Here’s a simple method to deal with varying intensities in a large run of images, assuming you have a known number of cells in a field. If I assume I should see, say, more than X cells per area, I can adjust my threshold to slowly increase…

Updating a used imaging system: Filters, Light Sources, LLG’s and More

Over time, every portion of your imaging system will begin to show signs of wear. Over a few years and a few thousand hours of use, you may not notice the small changes occurring in your system, but they can add up to a major performance…

Free iPhone to Microscope Adapter…

If you have access to a 3-D printer, you can make the following adapter for the iphone! -Austin

Making a microscope from binoculars

Last month a friend gave me two old pairs of field glasses. One set was US Navy issue, which has the old-school build quality of a tank, and produces a bright, sharp image. The second pair was cheap and damaged. I’ve considered what to do…

Obvious interest in home 3-D printing

I’ve been following the success of the PrintrBot on kickstarter, and it’s amazing to see that the project is now 3,000% funded. Numbers like this show how many people are interested in making things at home. I think this will likely be…

2,100 hits and counting!

Today I saw that I’ve received more than 2,100 views in the past 30 days. I just wanted to say thanks to those who read my blog. I hope 2012 will be a growing year for the site and for our industry. Thanks for reading – Austin

DIY Stereo Microscope

This looks like a fun project. The guide shows how to build a focusing system, which I’d likely avoid due to the time involved, and the relatively low cost of focusing blocks on the market. This would make a nice little home use stereo…

Nikon “Lambda” lenses – what are they and does it matter?

Over the past year, Nikon has quietly begun replacing it’s “CFI” objectives with new “Lambda” coated lenses. The Lambda coating on these lenses is referred to as a “nano crystal coat”. The developers state that there is a spongy type of…

Prior Motorized Controller for Ti Filter Cube Changer

Prior has released a nifty solution for those wanting to motorize a basic Ti microscope. The Ti scope doesn’t usually include a “Hub” when it’s sold in a manual config. The hub is quite expensive, so when people look into upgrading to a…

Use your iPhone for Microscopy

This is a great concept!

A followup to my CNC machine build

Can be found here… – Austin

Light Blocking Darkbox from Technical Instruments

Microscopists frequently work in the dark, in order to keep background ambient light out of our images . This means we need curtains, dark rooms, and even custom monitor color configurations in order to drop the room light for imaging. If…

Do lasers last forever? What to know before buying a launch.

My company has been selling integrated and stand alone laser systems for about a decade now. Over that time laser use has drastically increased, but laser manufacturers have been slow to respond to the market demand. The state of the laser…

UCSF Mission Bay at Night

One of the perks of my job is that I get to work on the beautiful campuses in the San Francisco Bay Area. I took this shot last night in front of genentech hall, using the Panorama 360 app.

How TIRF works on a Microscope

TIRF is a widely used tool for effectively creating a super resolution instrument out of a standard widefield microscope. The cool part of TIRF is that it bypasses the limits of axial resolution on the scope not by altering the optics…

Solar Timelapse

This is just amazing… -Austin

Update on Andor Neo Camera

I had an opportunity to demonstrate the Neo camera on site with a customer yesterday at UC Davis. We captured some great images of GFP tagged pathways on PKC cells. We were able to image the cells at exposures down to 1ms @ 2×2 binning…

Neo camera at 100fps

Andor’s Neo camera has been out for about a year now. I first wrote about using it back in February. The camera immediately showed the major difference in field of view between sCmos sensors and traditional interlines quite well, but the…

Hands on with Imaris Bitplane

During my company sales meeting I had the opportunity to receive training on Imaris Bitplane, which we are now able to sell in our dealership territory. I’ve come across this software package off an on over many years, and have always…

SOPA Protests by Google and Wikipedia

Today both Google and Wikipedia have altered their sites to protest SOPA/PIPA. I can’t think of a time before where something like this has galvanized the internet community. I hope the US congress can listen to it’s constituents…

1,500 users in the past 30 days!

I just wanted to say thanks to all of my readers for helping me generate 1,500 hits on the site!I hope to continue to grow this site as a resource for the microscopy / imaging community in 2012 and beyond! -Austin

SOPA and the future of the internet

I don’t normally post on political subjects here, but I believe, along with Google and many others in the online community, that the progressing “SOPA” bill carries a major potential for government censorship of speech. A line by line…

Kickstarter’s 2011 Highlights

I really enjoy browsing Kickstarter projects, both to see what investments are available and also to share in the inspiration and passion of so many inventors and creative thinkers. Here are the 2011 highlights

Attend a Scientific lecture at the Bar?

Wish they did this in the US. http://www.haaretz.com/culture/israeli-bars-get-smart-as-academia-finds-an-unlikely-late-night-home-1.404331

For those of us trying to get back to family today

Yes, it’s sappy. Yes, Rascal Flatts is more pop than country, but dang these guys can sing. Wishing all of my friends, colleagues and readers a Merry Christmas, and Happy Holiday Season. httpv://www.youtube.com/watch?v=iW8wMMIVBFM

Merry Christmas! More Snowflake images from SEM and visible scopes…

I guess this has become a yearly tradition, so once again here are some beautiful and curious SEM and visible light snowflake images.

InVivo Environmental Chamber Manuals

Have been added to the resources section for download.

NIS Elements Fix for Sutter products Released (NIS 4.0)

NIS 4 was released about a month ago, and the US dev team has already released a DLL fix for the Sutter Instruments product line, which I’ve uploaded here. Don’t use this unless you are running NIS E v4, AND you’re seeing a crash when…

Image Bit Depth, and why your pictures don’t look good in Photoshop. – Episode 3

Over the last week I wrote about image structures, bit depth, and some of the difficulties of how images are viewed on our display systems. Today I’ll wrap everything up, and answer one of the most common questions I hear, “Why does this…

Image Bit Depth, and why your pictures don’t look good in Photoshop. Episode 2

In my last post I explained how images are really three dimensional structures inside of your computer, and what exactly bit depth is. Today I’d like to finish up discussing how this boils down to trouble in viewing, saving and in general…

Science working for the greater good…

Andor has a news/ad up on how one of the spectral imaging systems they sell can keep away those pesky scotch forgers. 🙂 My favorite line on this blurb is, “Quality standardisation for Scotch whisky is assessed using alcohol content…” Heh…

Image Bit Depth, and why your pictures don’t look good in Photoshop. Episode 1

I’d like to cover today an essential aspect of imaging, that a surprisingly large amount of scope users either aren’t aware of or are only partially familiar with. Image Structure While we view images as two dimensional constructs, we are…

Well, it must be a stressful job…

Then again, that’s what taxis are for. Considering how hard the FAA is on pilots who get convicted of DUI, I’ll be curious what kind of treatment he gets. FAA Administrator Charged With DWI In Va., On Leave From Work

Goal Zero Solar System – Review and Support Experience

I recently received a Goal Zero “Guide 10 Plus” solar charger and battery kit as a gift for my birthday. These units combine a ruggedized solar panel with an elegant electrical distribution package, intended for outdoor use in harsh…

Chemistry makes life safer and easier…again!

This company is marketing what they call a “Super-Hydrophobic” compound. My interest is related to how this may repel ice on the Cessna. Ice is a serious concern for small piston aircraft operators like me. When the weather is bad we are…

The Olympus Saga Continues

Reuters is reporting that ongoing arrests related to some Board of Director Members could take weeks. It’s yet to be seen how the shakeup at the top and the corresponding valuation changes will affect the company’s microscopy division.

NASA Timelapse from ISS

This is amazing. These were taken using a high sensitivity camera developed for the mission. Earth | Time Lapse View from Space, Fly Over | NASA, ISS from Michael König on Vimeo.

Site Changes

I hope you like the updated site theme and menu structure! I still need to fill in a lot of the menu structure, but I’m trying to make it easier to browse tutorial-related posts vs. random news and observations. Please let me know what…

Using Image Analysis on H&E Slides

This is a tough problem to solve: How does one analyze quantity of stain on an H&E slide? The fundamental problem with conventional thresholding has to do with the tool function vs. the expression of the stains. Any threshold tool one can…

The CNC Machine is done!

So after 6 months of watching the guys at mydiycnc complete their manual, and roughly 4 months of building, I’m happy to post that I’ve finished the machine. I’ve written an extensive post on the last few days of building, on the build log…

WHY YOU SHOULD ATTEND THE UCSF/QB3 Microscopy Course

Over the course of my career, I’ve flown across the US to attend a variety of imaging related instructional courses, all on the eastern seaboard. We are all familiar with the Woods Hole courses, the AQLM course, and so forth. What has…

Google Barrel Roll?

Sorry posting has been light – busy busy, and I have a lot of fun stuff and news to post as soon as time allows. In the meantime try this: Goto www.google.com in any browser EXCEPT IE, and type “do a barrel roll”. it’s a nice easter egg in…

Precautions on motorized focus systems and nosepieces on inverted microscope

Again today I had the distinct horror of knowing that – should I follow “established procedure” while working on a scope, I would damage the prime lens of the objective in use. In this case the cause was simple: Many microscopes use an “in…

What’s next for Olympus?

I’ve been watching reports like this for the past week with interest. I guess we’ll have to just wait and see how this unfolds, right now I think it’s too early to know what the truth really is. -Austin

Best Bicycle Safety lights ever!

Here’s another inventor who used micro financing to get his idea to the next level. I think this is a wonderful idea for so many reasons. It’s elegant, uses disruptive LED technology for numerous advantages and integrates onto an existing…

DIY Open Source Fusion? I really hope this guy can pull it off. What a worldwide change it would be!!!

If we don’t support a guy like this – who will? Chevron? Valero? The next time he opens up a funding round, I’m going to jump in. I’ll keep this on my radar… -Austin

Throwable 360 degree panoramic camera

This is an excellent idea! To add to it I’d increase the padding, and supply it with a small surgical tube launcher. A pic from say 25-50 feet up would be really cool for a lot of different scenes…

Identifying vibration from on-scope sources

Blurry images can be caused by more than optical problems. I recently had a customer with a rather complex system tell me she was having focus/blur issues on her scope. When I inspected the system I found everything to be fine on the…

Coupling a C-2 confocal to an AZ-100 zoom scope

I recently worked on a demo where the customer wanted a confocal with magnification range from macro (1x) to low power compound levels (200-400x). In order to meet this requirement we showed him the AZ-100 zoom scope, and the C-2 scanning…

Basejumping with a wing suit

This is just amazing! httpv://www.youtube.com/watch?v=kApK2MlwYBU

HDTV Antenna from CoatHangars, Tinfoil and a 2×4

Well, this is another non-microscopy post, but it does have something to do with “imaging” in a general sense … About 3 months ago i turned off my satellite TV programming, for two reasons: One, I watched too much TV. Two, it’s a ripoff…

Update – High Speed Scanning with an ASI Stage

A few weeks back I posted that I would be testing high speed stage movement with an ASI stage. Of course things are never easy to actually get working, but I managed to, and here are the results: Triggered camera ( I used an Andor Clara…

Aurora Australis from ISS

This is an awesome timelapse! I’ve dreamed of one day seeing things like this from space. Maybe developments like the private SpaceShip Two and SpaceX this dream could one day be realized. Alas, I’m quite confident the ticket for a ride…

Why every live cell imaging system should include a rack server

Well, yes I AM biased, but here’s the scoop… Look around your microscope… What do you see? Small control boxes, Ac/Dc power converters, expensive components sitting on the floor. Is this really how an instrument should be built? I say no!…

I’ve made a lot of progress in building my CNC machine

You can read about it on my build log here. Feel free to email me on where to find supplies for one of these cookies. They are readily available if you know where to look! -Austin

Breaking the speed of light?

This work hasn’t yet been published in a journal from what I can find, but the preliminary results are interesting… Faster than Light Neutrinos?

Fluorescence used in live surgical applications

This is an excellent idea as a marking aid for cancerous areas. Hopefully it’ll expand to more cancer types. Now if one could couple this to a 3-D scanning system which used a laser cutter…

SETI Discovers Planet orbiting Binary Stars

This is just cool from a Star Wars geek point of view. Of course I have to link to this clip from Start Wars IV. Probably one of my most favorite clips ever… httpv://www.youtube.com/watch?v=wEUGF3NGbPg

Laser Pointers and IR Damage

I recently discovered through the EverydayScientist that those cool powerful green laser pointers we all like to play with may be putting out IR on the same line! A study performed by the NIST found that some of the commonly sold green…

Wish they had this in the US!

Researchers’ Night in Europe

Memory Size Limits in Elements and Progressive Loading

If you stitch large images, you’ve likely seen the “Image will be Loaded Progressively” message when loading a stitched file which has a size greater then the computer’s available memory. Why do stitched images have size limits, whereas…

Flexible OLED display from UCLA

I want one! -Austin

32 vs. 64 Bit Imaging Options

Windows 7 x64 has been officially on the market for 2 years as of this month. In that time almost every device manufacturer has added support via x64 drivers. Of course, as I say this, there are a few notable hold-outs, so before you…

P-38 and a window to the past

Normally I don’t post things like this, but I had the opportunity to watch a rare P38 lightning fly at my local California Capital Airshow. The P-38 was a magnificent aircraft, and one of only a few twin engine fighters in WWII. The pilot…

Updating Software? A pre-chaos checklist…

A few years after your shiny new system is installed, you’ll inevitably look at it just like you look at a car. What was once running flawlessly now has a few bugs, some dust, is slower and generally worn in. So, at some point you’ll…

Batteries need more charge – is this the answer?

Looks like promising research! If this estimate of an 8x increase in storage capacity is correct, it could revolutionize transport, as this is the missing link to electric propulsion. -Austin

Lumencor Sola Driver for NIS Elements

Yesterday we received our first shipment of Sola white light LED driven sources for microscopy. I had a chance to snag one and write a driver for it. Price is $300 USD. The driver controls both the shuttering and ND on the box, and…

PhotoFluor 2 Driver for Nikon Elements

89 North has asked me to cook up a driver for the PhotoFluor 2, which I am now hosting under my Macros & Journals page, or you can use this link. This driver works in NIS Elements AR, and BR with Advanced Interpreter. Please contact me if…

Simple Low Cost Method for Laser Fiber Alignment

If you have a laser launch, you may wonder if the launch is putting out the same level of power it did as the day it was installed. One of the difficult aspects of using a laser launch is that the single mode fibers required for launching…

More on LED Engines – Updated comparison against the Sutter DG-5

About a month ago one of my coworkers, Aaron Lum Ph.D and I, had a chance to compare various light sources and to measure the power they provide. Most importantly, we were able to compare LED engines against other conventional light…

Extremely simple and inexpensive handheld camera mount

There have been quite a few times I’ve simply placed my iPhone camera into a microscope ocular, so I could snap an image of an affect I was seeing. Along the same lines, this is a PVC pipe-connection for your run of the mill point and…

The Highs and Lows of Working for Research

So last week started off rather rough. About three months back I helped a customer avoid a software restriction, by replacing a controller card inside his computer. All went well, the card did it’s job, so on I went. It turns out that card…

Why is it STILL FUZZY?!?!

Chris Murphy from Q-Imaging sent me this (Thanks Chris!). Poetic… httpv://www.youtube.com/watch?v=vHjuV7kRpFQ -Austin

High Speed Stage Testing

Will be testing a high speed stage scanning method in the next few days, and will publish the output I get. ASI has some special firmware inside the stage controllers they use, that allows for high speed scanning. They also have 8 slide…

NIS Ar B728 Released

Some new features and info, available on the download site here. Note that your username can be anything, but your elements key ID# is the password. -Austin

Laser Emission Test Block

So I came up with an idea for this a few weeks back, while in a training at one of my suppliers. At trade shows people will attach a sanded-plexiglass rod or similar to the output of whatever light source they are showing. This allows…

Nikon Ti-E TIRF Fiber coupler alteration

One of the nice features of the Nikon TIRF arm is that you can easily modify the input coupler for the laser fiber to accept flat or angled fiber couplers. Instructions to do this can be found here, or on the files and info page. -Austin

NIS Elements 3.22 Download

You can find NIS D, along with AR, BR and other modules, at nikon’s download page here. You’ll need your HASP ID for the login, which can be found under start->Programs-> NIS Elements -> HASPinfo on your computer. I’ve added this link to…

ASI Stages and Camera Triggered High Speed Scanning

One of the limitations of current software packages is the delay time to move+capture images between the camera and a stage. Most of this is based on the software and it’s requirement to communicate closely with the stage and camera. ASI…

The death of the company office?

Reading this article has brought up a subject I’ve long thought about. Is a physical office structure still relevant in the wake of today’s technology improvements? Normally I work in two locations: At a customer site, and at home. When I…

Fiber inspection and cleaning – why it matters!

Laser launches that rely on fiber coupling are awesome. There is no need to physically shoot the laser or lasers into a microscope via optics alone. Instead the lasers are delivered into a fiber, and then the fiber can be connected to any…

Convert an iPhone into a microscope, help save a life?

One can easily imagine the elegant simplicity a web-connected low cost, mobile microscope could bring to field medicine. Here is some excellent research demonstrating a simple microscope and simple spectrometer conversion using an iPhone…

Lumencor Spectra Driver Available

I’ve written a Lumencor Spectra Driver that works with NIS Elements B3.2+. (AR or BR + Advanced Interpreter) The driver provides integrated control into elements for both intensity of lines and channel. These appear as a shutter and two…

How to Align a Dualview 2

Walking through the alignment procedure of the DV 2, narrated by Jeff Harris from Photometrics . Great video and great explanation Jeff! For those of you who have a DualView, I’m certain this video will come in handy…

The inventive founders

I sure wish we had political leaders today with an industrious, inventive approach to things these days! http://blogs.forbes.com/alexknapp/2011/07/03/the-five-best-inventions-of-the-founding-fathers/

Light Source Shootout: Intensilight, Photofluor, Spectra, Heliophor and Sola

Overview Over the past 12 months, several new LED driven light engines have been released to market. I’ve posted on a few of these systems a while back. The big question here, more than anything else, is how much light do these boxes…

To our Entitled Youth

I visit a ton of labs, and it is becoming increasingly clear to me that the subsets of entitled researchers are growing. Our generation (and I use “Our” lightly) has become accustomed to getting a lot for a little. It is very easy to…

What would you like to read about?

I’m interested to know what people like to read on my site. Please take a second to respond to the poll below. I’m also quite interested in your feedback! What new subjects or areas would you like to see reported on here? How can I help…

Nikon Oils, Perfect Focus and What to Use

There are two docs published by Nikon regarding the use of oils. Most people think you can use any old oil for any microscope, but this is not the case. Zeiss, Leica, Nikon and Olympus all have specific chromatic, spherical and viscosity…

Confocal vs. Widefield

I’ve recently received several questions regarding what a confocal does that makes it better than a non-confocal fluorescence microscope. I figured it may be helpful to answer this in a post, so: Both the confocal and the widefield…

Desktop CNC Machine

About 6 months ago I invested on kickstarter, in a project that would ultimately launch a company for a fellow in Placerville, CA, and would provide me a set of plans for a desktop CNC machine, built at home. After a huge amount of effort…

Ti-E Perfect Focus Usage and Troubleshooting

The Ti-E PFS is an excellent automatic focusing system. Using the system hinges on one key aspect: The NIR LED used for focusing. The PFS is basically a laser reflection system. A near IR LED is delivered into the back of the objective…

Very Large Telescope night timelpase from Chile

This is the best use of YouTube I’ve ever seen. Amazing!!!! httpv://www.youtube.com/watch?v=wFpeM3fxJoQ The use of CCD cameras in science was basically pioneered by astronomers a few decades back. Cool to see these instruments in use and…

Acquisition crashes, and power settings in Win7

Windows 7 has a new power management interface, and the design of modern motherboards, along with win7 Automatic Power Management (APM), can cause some insidious device-based software crashes if power options aren’t set correctly. Here’s…

Good thing I drink a lot of coffee…

They didn’t employ any imaging in this research, but it’s an interesting study, and one I will use to justify my massive coffee intake… – Austin

This Saturday is International Learn to Fly Day!

So if you’ve ever wanted to see what it takes, check out a place where you can take an intro flight here. This is a picture my Dad took of me during my primary flight training in 2002. He met me at Modesto, CA in his plane (the red and…

Sutter Smartshutter cable extensions – don’t use a parallel cable!

Sutter instrument filter wheel controllers can run a wide array of devices. Using a Sutter 10-3 it’s possible to run 3 wheels, and 2 shutters. all on a single controller. now when it comes to connecting things, there is one way you can…

Will visible spectrum imaging play a part

In a real “tricorder”? The X-Prize is looking to hand someone $10million USD who can cook up a solution to the need for a field medical scanner. Considering the impact the x-prize had on manned private spaceflight, I’m looking forward to…

What happened to the “Shade Tree” Mechanic?

This isn’t an imaging related post, I admit. I figured Id share my experience this weekend with my readers as many of us are lucky to have a car, but tackling maintenance issues can be a scary thing, and the shop sure charges a hefty price…

NIS Elements Viewer for Mac OS

Nikon has finally released a Mac OS compatible viewer for ND2 files! You can download it here (updated link!) And I’ve added it to the files & info page. – Austin

Generating Great 3-D Images with NIS Elements

Want to make movies like this? httpv://www.youtube.com/watch?v=qAVKzbq3DkY NIS Elements has a nice 3-D movie export/creation function. Getting into the 3-D mode can be a bit challenging, so here’s a simple guide to producing a great movie…

Back up your NIS Elements settings! (V3.1+)

(Updated 5/6) – One of my colleagues (Thanks Aaron) noted that the exporter/importer only works on v3.1 and higher. So in the past week I’ve had two systems that mysteriously lost all device settings from elements. I am suspecting this is…

Voltage output from NIS Elements, MetaMorph or uManager for under $200

I posted briefly about this a while back, in my explanation of the demise of the parallel port. I finally got my hands on a National Instruments USB-6008 box, and have found the unit to be 100% compatible with any NI-DAQ controlling…

ASI MS-2000 Flat Top Stage

Apparently ASI has had a flat top variant of it’s MS-2000 stage available for a while now. News to me! If it’s anything like the current stages they sell I’m sure it’ll be a frequently recommended product from me. – Austin

Measuring object angles using ImageJ/Fiji

I had a question posed by a coworker who wanted to identify the rotational orientation of an object. The object was a nucleus, and the orientation was indicated by the position inside of the nucleus of the Golgi. The cell in this case was…

Finally – An answer to the Incadescent Bulb?

I’m a man of the fence when it comes to incandescent lights. I’m also probably one of the most dynamic users of illumination technology in all of it’s forms. I regularly use lasers, xenon, metal-halide, mercury-gas, incandescent, LED…

Lens Free Tomographic microscope

The Ozcan Research Group, based at UCLA, have been working for a while on miniaturizing microscopes, for a variety of applications. In this newest paper they describe a method of microscopy that alters illumination to achieve resolution…

iPhone Tracking and options for removal

So there was big news the other day revealing that the iPhone tracks your location and sends that data to Apple. Of course all my buddies with Android phones were rubbing this in…until today! HA! But the bottom line for me is that I don’t…

Nikon C2 – NIS Elements and Spectral Capability

Nikon has redesigned and updates it’s classic C1 Confocal. The C1 was a great core facility confocal as it was a stable and reliable product. The one thing that held it back was the lack of access to NIS Elements software. With the release…

Near IR Imaging using the Spectral Applied Research Borealis Mod

Spectral Applied Research is a custom optics house based in Ontario, Canada. My company was lucky enough to find out about them through one of our customers, and we have been working with them now for about 5 years. Spectral has a history…

Elements 3.22 B 725 Now Available

I’ve uploaded the major installers to my site for easy access: NIS-E 32 Bit Installer NIS-E 64 Bit Installer – Austin

Compressed Sensing and Single Pixel Cameras

I have a friend with a PhD in signal processing, who sent ,me this interesting technique of using image compression algorithms in combination with a DMD, to generate spatial images from a single pixel! Very cool setup, there is another…

Proper RGB Conversion of Multichannel Images

When acquiring images in NIS Elements, it is possible to acquire each image with a color over that is approximate to the wavelength used for acquisition. This is the easiest way to view and relate multi-channel data, but when converting…

Nikon DS U3 Series Controller Install Guide

The new Nikon controllers for DS Series Cameras run on Firewire. As with other firewire adapted imaging cameras, there are numerous small issues to awtch out for during the setup and operation process. Once they are up and running, they…

Testing the linearity of a camera using the Camcal CC-560

Numerous camera manufacturers claim **% nonlinearity on their sensors. Are you certain that this specification is accurate? One way to test this is to simply increase your exposure time against a constant emission source. The Camcal CC-560…

The reality of “explosive decompression” on large aircraft

This is a bit personal for me as I’ve flown this exact flight numerous times when working for a Tucson-based company. This flight experienced explosive decompression, which basically means the pressure-holding chamber (the aircraft cabin)…

I Guess I need to eat more good cholesterol…

Recent research indicates that good cholesterol may attack cancerous cells directly… – austin

360 panoramic from an Iphone

I took this very nifty 360 degree panoramic image using Occipital’s 360Panorama app for iphone. I have an iphone 3gs, which means no gyro and a lower sensitivity camera, and the image still turned out amazingly for a 20 second spin! I’d…

Nikon Ti-E Hub Firmware v4.00

Are you having problems using some of the functions on a newly shipped Ti-E? It turns out there are several problems which can all be cured by a simple hub update. All of these problems stem from a firmware mismatch between the scope body…

Determining background sources in fluorescence

For microscopy engineers and suppliers like me, the background produced in an image is of importance, if that background is created by the imaging system itself. What so many of us on this side of the scope (vs the user side) forget to…

Voices from the past….

I found this a few months back on the wall of the FBO at Oroville Airport, CA. For those who don’t know Doolittle was the guy who pioneered the use of aircraft in the US Navy. Yeager was the man who first broke the speed of sound in the…

Texas Instruments manufacturing plant damaged in Japan earthquake

It looks like the manufacturing facility which makes some of TI’s CCD’s was affected in the recent earthquake. TI manufactures some of the CCD’s used in cameras for research. Austin

Photometrics LVDS cards on Win7

I recently slogged through a tough install with a customer (Thanks Sean!!) in an attempt to run an older Photometrics camera using a PCI card in windows 7/xp. What we found was that the latest driver, (as of this post v. 2,7,10) is not…

A life of learning

Just a simple thought tonight: When I was a kid many of my friends would comment in a disparaging manner that I was always involved “working on electronic junk” or similar. Isn’t it interesting how this hobby (along with astronomy) has…

Lab PSU from a PC ATX Power Supply

So I got around to making a personal lab power supply from an ATX power supply from an old computer. Who doesn’t have a few old PC’s laying around, right? So after pulling the PS, here were the steps to getting things working: Things…

I’ve moved to Bluehost – Notice?

So after experiencing extremely slow delays (page load times) with my old hosting provider, I decided to move to Bluehost. For those of you interested in running your own wordpress site, it turns out that some companies don’t host…

Prior Slide Loader Running on a Nikon 90i Upright Scope

Here is a video I shot last month of a Prior Slide loader being coupled with a 90i microscope from Nikon. Normally the #1 issue with loaders is that they aren’t mechanically stable when coupled to the scope, causing constant adjustments to…

How to use Orthagonal Viewer in Elements

NIS Elements includes a standard orthogonal slice viewer, but another neat feature is the standard Xz/Yz maximum intensity projections available. Here are the steps to get the most out of this view: 1 – Open your Z Stack in Elements. 2 –…

More on Device control via TTL, Voltage and the death of the parallel port

So a while back I cooked up an overview of how to control TTL devices using elements, meta or other software through the parallel port. With the release of 64-Bit version of Windows, it’s become obvious that Microsoft will allow the…

LED Light Engines for Microscopy

Once LED’s became powerful enough for use in applications like traffic signals and bike lights, every microscopist has been wondering when they’d make their way into our corner of the world. Today there are several options for LED based…

*UPDATED* Micro-Manager Tethered to a Nikon Digital SLR

***UPDATE 3/3/2014*** After a few requests for a report on x64 capability using this tethering technique, I tried installing the NK Remote software on a rather fresh copy of Windows 7×64 – it did not communicate with the camera at all. On…

Returning to the Joy of Flight

Aside from my interest in imaging and microscopy, I am an avid lover of all things involving flight. One of the big problems in the world of aviation is the daunting task of acquiring a pilot’s certificate, and the other is the regulation…

Our Love Hate relationship with the sun…

Thought this was an interesting perspective on our friendly star…The aviation world is well aware of the effects caused by solar flares, and we don’t yet have an answer for this! – Austin

Andor Neo sCmos Review

Last week I had an opportunity to do a direct comparison of a Neo against a “competitive brand” IXC-285 based camera. Here are some of the results: Installation of the camera: It’s important to note that the high speed data transfer card…

Fix for Elements v 3.2 and ASI Stages

As anyone who is running NIS Elements v 3.20 + is aware, the ASI stage controllers of any MS-2000 series will not be usable once elements issues a connection command to the controller. Elements will control the stage properly, however the…

Check your Intel processor!

Intel recently released a MAJOR announcement about it’s chipset. To know if you are affected, check the link or you can follow this simple two part check: 1. Was your computer purchased after jan 9, 2011? If no, you’re safe. If yes: 2…

Multiple Voltage Power supply for $10

I’ve been searching for a selectable-output power supply to use in my work and home projects, and came across this instructable. Will be making one up as soon as I have the free time! For anyone working with LED’s or triggering or really…

Kymograph for Velocities

I had a customer interested in some rather tough mitochondrial analysis. None of the tools he had available were working. After some homework we found that the kymograph tools provided by J. Rietdorf and A. Seitz included a full velocity…

Save As TIFF in Elements During ND Acquisition

If you perform offline analysis on image data acquired in Elements, you probably have found that working with the ND 2 file in any other application can be touch and go. Luckily, Nikon provided a very robust save function in Elements that…

Imaging in Your Language

Recently I found a tool which helps to plot the locations of site viewers. Based on the global interest in this work I’ve added a translation plug-in called GTranslate, which should support live Google translation in 98 languages. I hope…

Merging multiple channels in Fiji

I had this question asked at my recent Bio-X training, and wanted to provide a thorough answer to it, as this is a common need: Assume we have multiple images, or multiple stacks, and we want to analyze something like the intensity through…

BioX Training at Stanford

Welcome Bio-X Course Attendees! Due to it’s utility and ease of providing common tools in a variety of operating system choices, I’ll be running this course using the FIJI build of ImageJ. You can find Fiji here. Please bring the following…

Pop Sci’s Most Amazing Science Images of 2011

I liked the simulated black hole myself… You can find the others here.

For All Imaging Applications in Windows 7 – Run as Admin

Windows 7 uses an enhanced security policy. This policy tends to disallow program access to sensitive parts of the operating system like the registry, unless explicit permission to do so is provided by the operator of the system (you)…

NIS 3.2 User Manual

Has been added to the Files and info page here.

Parallel ports wont work in 64bit windows!

After speaking with several software vendors I’ve learned that win 7 64 bit will not operate a parallel port with any device automation software. So gone is the ttl access needed for so many of our devices! Fortunately there are low cost…

Andor Resleases Neo sCMOS Camera

Andor has released a new version of it’s sCMOS camera. The Neo camera provides a major noise advantage over traditional CCD systems. httpv://www.youtube.com/watch?v=AWCdoDZvOqQ&feature=player_embedded

Nikon Epi FL Cube Tables

Nikon did everyone a favor by creating unintelligible names for their fluorescence filter cubes. As a result you may have a cube that reads “UV-1” but will have no data on the ex/em or barrier specifications. So here’s the entire…

Use ONLY Hard Coated filters on a Lambda XL!

I recently learned from Sutter that only Hard Coated filters, such as Semrock or Chroma ET series. If you have already purchased a non-ET set for your XL remove it quickly! Here are some examples of what will happen otherwise… Update –…

How to remove and install filters on a Sutter Instruments filter wheel

I keep getting asked this so I figured I’d write up a how-to. When using a sutter wheel it may be necessary to remove, replace add or reposition filters in your wheel. A good example is repositioning filters to provide the best wheel…

Fiji – an ImageJ build for the Life Sciences Community

Fiji (not the island :-)) is a distribution of ImageJ that includes a large variety of life science import/export functions and tools. If you are looking for free, simple analytical tools this is definitely one to try. You can check out…

Improvements to Andor’s EMCCD Cameras

Andor has announced an updated line of EMCCD cameras. The new cameras include photon calculation capability, firmware improvements, speed improvements and new auto tune type features to make controlling the various aspects of these cameras…

Measure noise in an ordinary DSLR CCD

While doing research for my future posts on how to use the camera calibrator, I cane across this excellent article on measuring noise sources in typical consumer digital SLR cameras. Very interesting results!

Collection of Essential Elements How-To’s

These are from Nikon, and include several key concepts of operation using the layers available in the software. I’ve packaged them in a ZIP for simple access here. They’ll be available in the files & info page as well from now on. -Austin

25 years of Confocal Imaging

Saw this on BioTechniques… A nice review of confocal imaging is available at Biotechniques website. – Austin

Instensity Calibration using a Photostable Light Source

I’m very excited to announce Technical Instruments’ first ever camera-specific calibration product! At left is an image of the CC-560, or Camera calibrator, which emits photons at 560nm. All of the cameras in the microscopy world rely upon…

updated Nikon DS Pixel Sizes

In case anyone is looking for the Nikon DS series pixel size, I have them listed under the specifications page.

Edit Device Settings for multiple programs easily using XML Notepad

NIS Elements, MetaMorph and a host of other programs rely on XML files to save settings that are user-adjusted inside the program. XML files are like mini databases that can be easily set up, modified and read by a host of programs. The…

How to Change a Lambda LS Bulb

Chris Ballard from Sutter Instruments has posted this Youtube video for changing an LS Bulb. It’s a great DIY reference to change a bulb! httpv://www.youtube.com/watch?v=GIr4IS6NBkk

Questions on Color Imaging

I’m cooking up a series of image conversion filters and explanations relating to color images vs. multiwave images. If anyone has questions related to this please email me so I can include them in the post! – Austin

SLR cameras for Microscopy

Most of the time, I work with people who need measurable and accurate (quantitative) results from the images they obtain. While this constitutes the bulk of my daily job, there is a much larger group of people using cameras on microscopes…

Running Micro-Manager with a Nikon TI Microscope

If you are running uManager you will need to install the Nikon Ti Drivers, as well as have a way of configuring the scope settings. You can address both issues by installing Ti Tools. You can find the most current version of Ti Tools from…

Mobile Support!

I’ve Added a mobile support plugin to the website for those of you living on the road. It’ll work with almost every smartphone/iphone/droid type of device out there. Hope you like it! Thanks to Alex King for the awesome free plugin!!! –…

Steve Jobs Explains Back Thinned Chips!

A few of my work colleagues pointed out the well presented positive aspects of larger pixel, back thinned sensors. If anyone has heard me prattle on about this they’ll find it familiar! Fast forward to minute 1:00 for the points on the new…

Split XY multipoints macro

Has been added to the free macros list under Macros & Journals!

Elements ND File Size Calculator

This is a calculator that will look at an ND experiment and tell you how large the resulting ND file will be. This is approximate and keep in mind if you are using the “save to TIFF” function the total size will likely be larger, due to…

How to Set Large Icons in Elements

This is useful for large screens that are using very high resolutions. Sometimes the icons are so small as to be hard to click and unreadable. Open Elements and select the View Menu, then Layout, then open the “Layout Manager”. Next select…

NIS Elements Stereo Zoom Settings

The Auto-calibration feature in Elements (beginning in version 3.1) is a great thing to have. You simply choose the objective you are working with, the software knows what camera you are running, so the calibration is calculated for you…

Micro-Manager 1.3 and Velleman Boards

If you are running micro manager and need to control a device via TTL or voltage, there is a nice driver written for umanager along with an inexpensive A/D card. The Card I used for a recent project was the Velleman K-8061. I’ve written up…

Bio-X Course Follow-up

Thanks to everyone who attended my first course on image processing (and acquisition as it turns out). As promised here are some links: – MBF Tools for ImageJ. This is a suite of processing and analysis tools, provided by the McMaster…

Quick Image Merge in Elements

If you want to merge multiple channels in Elements here is a quick solution: 1. Make sure you have the channel tabs activated. Do this by clicking the Edit menu, then Options. Select the “Appearance” settings. Make sure the “Show Channel…

Saving an image as you see it in Elements

If there is one simple question I get during training sessions it’s “How do I save an image, so that I can open it using Photoshop or other programs, and have the image appear exactly as it does in Elements?”. The reasons for this are…

Notes for the Bio-X Workshop at Stanford

If you are enrolled for the Bio-X Image Processing and Analysis Workshop, I want to make sure you get the most from the course. To that end: If you don’t have a laptop please find someone to work with during the course, so you can follow…

NIS Elements PFS Override when running ND experiments

When using the “Wellplate2” Macro with NIS AR you may have noticed a small but important limitation: Once you’ve loaded your specified sites into the 6D experiment, you can no longer make adjustments to the scope PFS offset. This means…

Elements release for Lumenera cameras

Here is the latest build for Elements if you are running a Lumenera camera. Follow the directions explicitly if you plan on updating or installing without a local rep available! Download

Technical Instruments Computer Specifications

I’ve added some PC spec sheets for each of the computer configs we sell. A few notes: 1. These show a monitor on them but this specific monitor is NOT INCLUDED. 2. The systems come with Windows XP SP3 (Which we will stay with until our…

Molecular Needle Bed?

This is an interesting method of delivering biomolecules into living cells. http://www.technologyreview.com/biomedicine/24347/

Dynamic Graph Output for Elements

Happy New Year! Laura Sysko from Nikon sent us a How-To on outputting live graphs that can be included with a timelapse or other ND file. You can find the How To Here.

Merry Christmas!

Here’s to a merry christmas and a happy new year!

More on Nikon SIM Microscopy

Details on the agreement between Nikon and UCSF for SIM can be found Here.

ASCB Roundup – Nikon Super Resolution and A1R-MP

Nikon dropped big news at ASCB when they announced the development of two new super resolution microscopes. Two different technologies were announced, STORM and SIM. The SIM technique was developed by Dr. Mats Gustaffsen, Dr. John Sedat…

ASCB Roundup – Hamamatsu Orca D-2

Hamamatsu has released a dual chip camera for ratiometric applications. The camera includes 2 of the ER-150 CCD’s, with one chip supporting discreet focusing, which allows the system to be chromatically aligned. Key features of this system…

ASCB Roundup – Andor Clara, Revolution Confocals

Andor had it’s new ICX-285-based Clara camera and revolution DSD Confocal on display. Key features of the Clara camera are: 1Mhz readout mode for very low read noise imaging Deep cooling capability at -45c Simple USB interface The…

ASCB Roundup – Prior Proscan 3

Prior has released a new Proscan 3 controller. This includes a new joystick which has some nice programming of it’s wheel functions. The controller supports TTL, Filter wheels, Shutters and XYZ encoded motors…

ASCB Roundup – 3i Vivo 2 Photon

3i (Intelligent Imaging Innovations) Has added 2 Photon capability to their live animal Vivo microscopy system, and they had a unit running at the show. Key features of this system are: Competitive Price point ($250-300k) Coupling ability…

ASCB Roundup – Sutter Lambda XL

Stopped by the sutter booth to check out the XL. It’s been out for a while but it’s always good to see. They had it running in a filter wheel loop for the duration of the show. Key features of this system are: 10,000 hr bulb lifetime…

Lambda XL Start/Stop Driver

I’ve added a Lambda XL driver to the free macros list that will enable the start and stop of the lamp from within Elements. This hasn’t been widely tested so give it a shot and let me know what you think! You can find the driver on the…

Upcoming ASCB roundup

I’ll be attending the ASCB conference tomorrow and will report on the latest technology available to our industry. I’m really looking forward to checking out the multi-photon systems now available!

Technical Instruments Macro Pricelist

A complete pricelist has been added to the macros and journals page. This is a menu of the standard plugins we have available for Elements and MetaMorph.

Neuroscience 2009 – Musicians hear better!

One of the presentations at the Neuroscience show in Chicago this year states that serious musicians are better at perceiving and remembering sounds than the average Joe. Cool stuff!

Elements 3.1 “App failure” after install fix

I’ve had an “Application has failed to launch” error after installing Elements on 3 new systems recently. Nikon has released a temporary fix until they update the installer. You can find the fix on my resources page or here is the direct…

Formable Mirrors for Microscopy

I’ve been waiting for adaptive optics to be used in microscopy for a few years now. It became a side interest when I read about the uses of formable mirrors in ground-based astronomy. It now looks like a few groups are using these mirrors…

Flash Memory for Imaging?

This article describes a novel approach to acquiring an image digitally: use flash memory! Some of the limitations described in the article are the lack of dynamic range (only binary data is acquired) however the small size of flash memory…

Tricks for Volume View and Deconvolution

Here are a few simple guidelines for deconvolution and presentation of deconvolved data. I’m posting them because it seems like I’m always forgetting one step or another, which results in waiting another 20 minutes for decon data to…

Fluorescent Microscope for a Cellphone?

Believe it or not researchers at UC Berkeley found a way to make it happen. It uses a simple excitation diode and emission system, coupled to a cellphone’s camera. They even have some examples of fluroescence! – Austin

Elements 3.1 Released

Nikon has released it’s major revision of Elements in version 3.1. (Build 587). There are several new features in this build and from what i’ve seen it’s quite stable. You can download the build here. – Austin

DXM-1200, 1200F and 1200 C Camera Compatibility – FAQ

A few years back Nikon released a very cool 12 megapixel stepping camera, called the DXM-1200. The camera was reliable and a nice product for many years. Unfortunately the march of time made a dent in this camera. The system, like many…

Video of Human Blood Clotting

I Found this while searching for a fluorophore. Very cool to watch on youtube!! Human Blood Clotting – Austin

Sensor Size reference Chart

Recently a colleague sent me a link to sensor sizes. Many of these are for consumer cameras, however the general references (1/3′, 2/3″ and so on) are helpful for microscopy cameras…

Pulse Control within NIS Elements 6-D Acquision

These directions will allow user control over an optical configuration to be specified at a given time-loop inside of the define/run experiment. So for instance if one wanted to trigger a shutter or light source to flash un-cage at the…

iPhone ResCalc Review

A few weeks ago I purchased an iphone. While browsing apps I found one that we can use in the research community! A company called Zem Dynamics (who also offers FRAP solutions for live cell imaging) has released a small app that can…

Copying Elements Settings for Multiple users

After installing a new imaging system it’s common to receive a phone call or email that goes like this, “The IT guys stopped by today and added our computer to our comany/university network. Now all of our settings are lost!”. Why does…

Andor sCMOS

This is a quick post – things are busy! Andor has a white paper and information up on a new “Scientific CMOS” sensor. Have they overcome the limitations to CMOS sensors for Scientific applications? This could really change the landscape…

Why do I want a low resolution camera?

These days it’s not uncommon to hear about consumer cameras with 10+ megapixel resolution. To the average consumer this seems like a good thing. How can more pixels be anything but good, right? In reality there are several tradeoffs to…

Elements Downloads

You can find the latest builds of Elements Here: NIS Elements AR or BR Build 548 NIS Elements D Build 548

Something Broken?

When a camera or a device isn’t working there can be any number of things wrong. How do we narrow the potential list down? I’ve taken a page out of my Toyota service manual and made a basic diagnostic flow chart which one can follow. This…

How to use Object Count in Elements

This is from the Nikon marketing group – excellent work if you are new to object count!Download PDF

Elements Build 548 Released

Yes this is a bit late. Things are busy these days! Elements B 548 can be found here if you need to download it. As usual back up all of your optical configurations and take screen shots of any filter configurations (i.e. if you are using…

Luminera Infinity 3-1 Review

Review of the Luminera Infinity 3-1 Up for review is a new Infinity 3-1 camera from Luminera. The camera is a new venture for Luminera as it uses a high grade monochrome Sony IXC-285 CCD. This is the same sensor used in many of the…

AVI playback with Elements Files

I’ve been asked by a few people what is the “Right Way” to export ND2 files to AVI. A lot of problems arise when the file is moved from the computer where the file is saved, to a different computer for playback (think your laptop for lab…

Lighting Control for Stereo Microscopy

When acquiring images through a stereo microsocpe one of the most common problems to overcome is inconsistant lighting. Whether looking at a printed circuit or looking at a natural specimen such as a fly most of these samples have the…

Photometrics Releases Evolve EM CCD

A few weeks ago Photometrics released a new EM-CCD camera tagged the Evolve.After attending a webinar presentation on this camera I wanted to point out the major technological benefiets of this system. Time will tell how these additions…

Elements SP 6 released

Nikon has released SP6 for Elements. There are several improvements for: Ti Microscope controls TIRF controls QImaging cameras ASI stages ND acquisition PFS control in ND acquisitions Macro controls in ND acquisitions There is a complete…

Stage Search Macro

Stage Scanning Macro for search and focus One of my customers (hi Paul!) asked me to make this macro a while back. Once I got into the design I realized just how useful this would be for basically anyone running an automated stage with…

What can programming macros do for me?

I’ve been running into a lot of programming applications lately. The fun part about using the Elements (or other) programming system is the amount of utility and flexibility it can offer to end users. Most people think about programming in…

Nikon Elements Software v3.0

For anyone using NIS Elements you are probably aware that v3.0 was officially released about 3 months ago. There are a host of new features included in this release and are detailed here. One addition that I’ve been recently very impressed…

FRET Calculations in Elements 3.0 This summary demonstrates how to calculate FRET crosstalk between samples and how to apply these corrections to a recently acquired FRET sample. Calculation 1. Calibrate FRET Images using samples loaded…

Microscopy 101

For the foreseeable future the compound light microscope will continue to be an anchor point in biology, metallurgy, forensics, technology, manufacturing and a host of other fields. Unfortunately it seems lately most educational…

Quick Resolution Calculations

Calibration is something people seem to remember after collecting a bunch of data. There is a simple calculation to use if you need to do a quick calibration or want to figure out a resolution/pixel size trade off. 1. Determine the total…

How to Clean Microscopy CCD Camera Windows

Disclaimer: Cleaning the sensor window is a delicate task and you can potentially damage your sensor forever, which most likely will not be covered by the camera manufacturer warranty. Please contact your camera manufacturer to determine…