vandermeerlab / HD-system-brainstem

Code for analyzing data from recordings in mouse brainstem head direction circuit.
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Quantify cell counts #29

Open stottbot opened 1 month ago

stottbot commented 1 month ago

Get quantitative cell counts of total NPH cells & total SGN cells for future mice with good DTN labelling. This requires taking zoomed in composites of all SGN & NPH slices and using something like ImageJ to count cells in each section.

Note: Max and Jalina did this in their papers but they didn't report the total number of cells. They made categories like <5, 5-10, >10, etc. So there is a gist, but not exact numbers for NPH vs. SGN cell counts. My labelling in NPH & SGN (when DTN is precisely labelled) looks much more precise than the CTB labeling in Jalina and Max's papers.