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scenerygraphics / sciview

sciview is a tool for visualization and interaction with ND image and mesh data
BSD 2-Clause "Simplified" License
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[wip] Starting to port Albert's scripts #505

Open kephale opened 1 year ago

kephale commented 1 year ago

Closes https://github.com/scenerygraphics/sciview/issues/373

kephale commented 1 year ago

I've started on https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/#find-peaks

I was able to get it running, but it is not the correct visualization yet. It currently looks like:

image

As you can see there are some scaling/offset issues to resolve. The script is also longer than I'd like, but I'm just trying to air it out for now. I also don't want this to use 3 separate volumes, but it was simply faster in this situation.

Tagging @acardona so he knows where the code is living.

kephale commented 1 year ago

Ok, find-peaks is fixed:

image

It is longer than the original, but still pretty clean: https://github.com/scenerygraphics/sciview/blob/albert-example-scripts/src/main/resources/sc/iview/scripts/find_and_count_cells_cardona.py

I didn't try to do any refactoring of the old ImgLib1 stuff.