![]() 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. Once you are finished click on 'OK', save your image, and you are done.1. ![]() You can adjust the size, color, and placement of your scale bar. The scale bar dialog will open and a scale bar will appear on your image. Click on 'Global' so that this calibration applies to all images that you open in this ImageJ Define the units of length in the 'Unit of Length' field. Fill in the 'Known distance' (in this case 5mm) without units. If you know your calibration values just enter the number of pixels in a known distance. (If you don't go to step 4 and you can enter the scale information directly into the 'Set Scale' dialog.) Select the straight line selection tool:ĭefines a known distance on your calibration image (5mm in this case):įilled in for you based on the length of the line you drew in step 3. Ĭalibration scale (ie a ruler or a stage micrometer) open the image.
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