![]() Latest build ( ) is failing on launch: ~ %. index.html,īut they aren't necessarily user friendly or well documented.I’m using an M1 as well, with Monterey. We are (slowly) building a library of macros here too. Other plugins you may find useful are at. ImageJ can do this too and label them, such as reporting independently for "White Pulp", "Red Pulp", and "Marginal Zone". This may be automated.įurthermore, let's say you need to manually outline different regions and have the counts described above reported separately per region. Histones in the nuclei stained with Alexa488 (green) and in a different channel the protein levels for each nucleus immediately outside the nucleus stained with C圓 (red). Or let's say you have all nuclei in one channel stained with dapi (blue) or DRAQ5 (far-red) and you want to know the intensity of We can modify this macro to do automated tasks such as this as you need them. Instead of processing each one manually, why not use a macro that will process the entire directory for you? Output as a montage of each channel with a merged image and a scalebar on each one in a format you could paste into PowerPoint. Let's say you have a directory with 37 images that were taken exactly the same way and you want them all There are also ways of changing the colors and contrast uniformly across datasets. There are more recent versions of Bio-Formats that work with more formats, but this works for all the Zen and Elements files I've encountered at work.Ĭlick here for a webpage primer on working with channels. The version of ImageJ running on my personal computer opens files from Zeiss Zen and Nikon ElementsĪs they displayed originally ( when you choose Hyperstack and Composite in the menu). It does not change the raw data but rescales each channel's display linearly. Import settings menu, raw data from most commonly used microscopes will open properly. With Hyperstack and Composite selected in the top left and bottom left of the ImageJ with Bio-Formats plugin opens raw data as they appear in the original software with the benefit of preserving the underlying raw data. ![]() I do this with the macros at collection_v100.ijm so that my most used macros & functions automatically load. This way, they will automatically load at startup. Optional: If you have a package of favorite macros, put them in the macros directory and rename the file "StartupMacros.ijm". I have it set to 12000 on my SurfacePro with 16 GB of RAM.Ĭheck the box Run garbage collection on status bar click. > Set for memory allocated to IJ images, this is going to vary widely depending on the sizes of your images and the computer you have. > Upgrade to: daily build Įdit > Options > Memory & Threads. Get it here įirst time you run Fiji, it may ask you to update. The file is named "bioformats_package.jar" and goes in the plugins folder in the ImageJ folder. You need to install the LOCI Bio-Formats so that you may open files If you have problems installing on Mac, please look here. Then follow Next Steps below for updating, setting memory, and setting up additional macro &/or plugins commands. You can even keep it on a USB key to run it anywhere USB drives work. Installation is just copying a folder containing a bunch of files to your computer. If you are on a network, make sure this is the local documents folder (unless you specifically want it on the network). Recommended: install in your documents folder. Also, recommend do not install on desktop, especially if your computer has a home drive on a network, unless you specifically want to be able to access from any computer anywhere. Unless you have full administrative permissions, do not install in the Programs Files directory or Applications (on ![]() Was my preference before 2020 but now I prefer Fiji. Fiji - comes packaged with many additional plugins of varying quality from great additional functionality to not well characterizedĢ.
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