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nel-lab / mesmerize-core

High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn
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Assessing the noise level before gsig_filt #259

Closed zhouyi0812 closed 7 months ago

zhouyi0812 commented 9 months ago

Hello! I wonder in the step of selecting the proper gsig_filt, if there is a way that can check the noise level for the original movie? And before and after applying the gsig_filt? Thank you!!

kushalkolar commented 9 months ago

gSig_filt has nothing to do with the noise level of the movie, I'm confused?

zhouyi0812 commented 9 months ago

I might misunderstood... I thought the high pass filter decide the size and number of kernel of gaussian matrix --> the filter apply on the florescence intensity on individual pixel, and smooth the low level frequency information --> the bigger the filter the brighter the pixel but lose more detailed info --> if the noise level is generally high --> we choose a relative big number of gsig_filt

kushalkolar commented 9 months ago

You want to choose a value that enhances - landmarks in the movie

zhouyi0812 commented 9 months ago

Which means the function of high pass filter in this case doesn't do anything about noise reduction or impact the low level info? emm...if so what is the different between choosing 3 and 5 if they both enhance the landmarks Thank you!

kushalkolar commented 9 months ago

If two different values both enhance the landmarks visually I would just try both and see which one works best, that's what mesmerize is for :)

The gSig_filt visualization helps with that.

kushalkolar commented 7 months ago

closing due to inactivity