Fiji 3d object counter in units

Hi everyone, and thanks in advance:

‘3D object counter’ plugin on Fiji extracts spots’ (i.e. objects’) coordinates in pixels (as far as I can tell from the output), I’m looking for a way to automatically extract these coordinates but by the stack’s meta-data scale (‘Resolution’), e.g. a spot that has the coordinates {“x”: 100, “y”:100} in pixels, and the Resolution is 10 pixels/µM will be extracted as {“x”:10, “y”:10}.
is there anyway to do so? if so, is it macro-friendly?

Hi @YishaiaZ,

there are the methods getPixelSize and getVoxelSize which can tell you how large pixels/voxels are. You can discover it by starting to type “getPix” in Fijis script editor:

The links are clickable and bring you to the online documentation :wink:

Furthermore, you can process the table delivered by the 3D Objects Counter using methods such as getResult. There is some teaching material online for working with tables: https://git.mpi-cbg.de/rhaase/ij_macro_gothenburg_2019/blob/master/03_ImageJ-macro_rois_tables_gui.pptx

Is that the methods you were looking for?

Cheers,
Robert

YES! thank you so much, that’s perfect.

BTW: I’m actually processing the tables as ‘.csv’ 's in python scripts. so your explanation is far more than what I needed. but it’ll be great for future generations :slight_smile: .

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