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labsyspharm / mcmicro

Multiple-choice microscopy pipeline
https://mcmicro.org/
MIT License
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MCMICRO from dearrayed cores #551

Closed josenimo closed 1 month ago

josenimo commented 1 month ago

Dear @Yu-AnChen,

I am trying to run MCMICRO from post-dearrayed TMA cores, the images were taken per core, and a WSI never existed. Therefore I have no masks for each core. Which seems to be a problem, the error that gets reported back is: No TMA masks in /fast/AG_Coscia/Jose/P18_TNBC/P18_E06_SL574//dearray/masks is there a way to bypass this need?

Thank you for the help

ArtemSokolov commented 1 month ago

Hi @josenimo,

Are your dearrayed images in standalone files? If so, you can just put them all in the registration/ subfolder and run the pipeline with tma: false (i.e., as if they are individual images) to process each core in parallel.

josenimo commented 1 month ago

Hey @ArtemSokolov, Thank you, I got caught up in the specifics, and forgot this could be done.