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labsyspharm / quantification

Quantification module for mcmicro
https://github.com/labsyspharm/mcmicro
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Added function for summing intensity values. #43

Closed FloWuenne closed 1 year ago

FloWuenne commented 1 year ago

Simple PR that adds a function to perform summing of intensities per mask.

User can activate summing by supplying --intensity_props mask_sum to the CommandSingleCellExtraction.py.

ArtemSokolov commented 1 year ago

Hi @FloWuenne,

Can you please rename the function to intensity_sum() to be consistent with other similar regionprops functions like intensity_mean(), intensity_max(), etc.?

-Artem

FloWuenne commented 1 year ago

@ArtemSokolov I changed the function name as you suggested!

jmuhlich commented 1 year ago

Can you also document this in the README under the --intensity_props option? That bit needs to be reworked now that we have a few of these extra properties but you don't have to do that in this PR if you don't want to -- you can just add a sentence to explain intensity_sum to the existing paragraph. I've filed #44 to remind us about reformatting it later.

FloWuenne commented 1 year ago

My last commit adds documentation for intensity_sum() and should solve #44!