Survey: What is your use-case for imglyb?

I am curious to find out how imglyb is used in practice. If you use imglyb in your research, please give a quick summary how you use it to combine the Python/NumPy and ImageJ/ImgLib2 worlds.

I know of pyimagej, for example, but practical use cases would be really useful for me.

Thank you for your help!

cc @kephale @ctrueden


Are you looking for use cases that use it indirectly as well? I.e.: people using pyimagej, and how they are using it to combine Java+Python?

Or are you only looking for cases of import imglyb directly in code?

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Thanks for asking, indirect use-cases are of interest as well. Really, any way that people use Python and Java now that they were unable to do before.

@hanslovsky I am using pyimagej to use existing imageJ apis/plugins within a larger python program. More specifically, I use it in a tool to export Electron Microscope annotations from the Thermo MAPS software ( and stitch the images around each annotation.

I am using python because the larger project is in python and I’m familiar with it. I decided to use pyimagej because the stitching of EM images is superior in Fiji compared to other python solutions like stitching using opencv. pyimagej allows me to integrate these powerful imageJ APIs into my python workflow. Also, it gives me the flexibility of using imageJ APIs that are very hard to find in other tools (e.g. changing image exif data like pixel size).