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petersaj / AP_histology

Histology processing
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Missing functions? #33

Closed RobertodelaTorre closed 5 months ago

RobertodelaTorre commented 5 months ago

Hi Peter,

I tried to use your code and the demo_histology_pipeline for aligning my brain slices; however, I can't manage to make the code run. I have the feeling that some functions are missing in the GitHub repository. For instance, AP_process_histology, AP_rotate_histology, AP_grab_histology_ccf, and AP_auto_align_histology_ccf. Some others might have different names. Is it possible that I cloned the wrong repository?

Thanks!

petersaj commented 5 months ago

That was from an older version of the code, I've removed demo_histology_pipeline from the current repo to clarify that.

The new version of the code puts all functions into a GUI toolbar that you run with AP_histology to make it more intuitive / get rid of the need to have a custom script - see the readme on the front page for directions

RobertodelaTorre commented 5 months ago

Thanks, Andy for your fast reply!

I tried the GUI at the beginning, but I couldn't see anything. That's why I moved to the old version. Now, I just found that there was a problem with the format of my images; they were not recognized. I tried now with a different format, and it works.