![]() ![]() ![]() see this post: Strange Issue with using BioFormats from python script in headless mode only.the need to automate opening CZI in headless mode required to write some kind of script and not using IJ.run method, because IJ.run and BioFormats do not work in headless mode.additional is sets the scaling for the pyramid level correctly, which did not work using the BioFormats plugin only (or I do not know how … :-)).the script allows you to directly specify the desired pyramid level to read.While it is possible to open them using BioFormats by choosing the correct image series, this is cumbersome to automate CZI image do have a pyramidal structure with different resolution levels.The reason why I created this script has several reasons. show originalįor most things just using the very powerful BioFormats plugin suffienct and will do the job thanks to work of the BioFormats guys and the the good communication with our DevTeam at ZEISS. # = "Autoscale", value=True, persist=True) AUTOSCALE # = "Show Preview Image attachment", value=False, persist=True) ATTACH # = "Show OME-XML data", value=False, persist=True) SHOWOMEXML # = "Open All Series", value=True, persist=True) OPENALLSERIES # = "Concatenate Series", value=True, persist=True) SETCONCAT # = "Read Pyramid Level", value=1, persist=True) READPYLEVEL # = "Stitch Tiles", value=True, persist=True) STITCHTILES You find the script here: sebi06/Tools_and_Scripts/blob/master/Fiji/scripts/czireader_complete.py # = "Image File", persist=True) FILENAME ![]() So feel free to use it and even improve it or share feedback. What I got is not perfect, but works quite well in most cases. Hi all, I am playing around for a while now with all the nice options on how to read CZI images in Fiji using python scripting. ![]()
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