Topic · 13 posts
ImageJ
13 posts on ImageJ, 2010–2026, newest first.
ImageJ posts, newest first
- 01 Mar2026
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…
ImageJMicro-ManagerNebula1 min read
- 01 Apr2016
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…
ImageJImagingMacros1 min read
- 29 Feb2012
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…
ImageJImagingMacros1 min read - 25 Jan2012
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…
Disruptive TechnologyImageJImaging1 min read - 07 Nov2011
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…
NIS-ElementsImageJImaging1 min read - 12 Sep2011
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…
NIS-ElementsImageJMicro-Manager5 min read - 23 May2011
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…
Device automationNIS-ElementsImageJ1 min read
- 29 Apr2011
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…
Device automationNIS-ElementsImageJ2 min read
- 29 Mar2011
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…
NIS-ElementsImageJImaging2 min read
- 11 Feb2011
*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…
Device automationDSLR CamerasNIS-Elements3 min read
- 31 Jan2011
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…
ImageJImagingProgramming3 min read
- 21 Jan2011
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…
ImageJImagingProgramming1 min read
- 11 Feb2010
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…
ImageJImaging1 min read