Austin's Imaging Blog

Category: ImageJ

  • Automated Capture and Save script for Micro-Manager

    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 of the images open in memory during a timelapse. Simple […]

  • 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 it’s aggressiveness until that minimum counted value is […]

  • 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 speed, binning, sub-array and bias clamp controls weren’t available. Over the past few firmware/SDK […]

  • 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 boggled my mind is that here I am in the SF Bay area, […]

  • 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 decide it’s time for an upgrade. This may consist of […]

  • 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 how to make sure your system is running in the best mode. Open the Windows Control panel Search for and […]

  • 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 application. What follows is an example of how to set this up using […]

  • 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 train on and talk about is the specimen side of the background. […]

  • *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 the other hand, the open source application “DigiCamControl“, worked perfectly. Now, as far […]

  • 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 stack A vs. stack B. We don’t want to convert the stacks […]