investigate pika ROI classifier - Githubissues

AllenNeuralDynamics / aind-ophys-utils

Repo for Ophys utils

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investigate pika ROI classifier #11

Open arielleleon opened 1 year ago

arielleleon commented 1 year ago

[ ] what are the inputs & outputs?
[ ] how does it work? what are the pros & cons?
[ ] how does it perform on current data?
[ ] what metrics do we want to track to evaluate performance?

Prior work on this:

https://github.com/AllenInstitute/LearningmFISHTask1A_data_validation/issues/32 https://github.com/AllenInstitute/LearningmFISHTask1A_data_validation/issues/34 https://github.com/AllenInstitute/LearningmFISHTask1A_data_validation/issues/11

MJD notes:

here are the slides describing the problems and Pika ROI classifier solution: https://alleninstitute-my.sharepoint.com/:p:/g/personal/michael_wang_alleninstitute_org/EdZX81Ffj9JGkWvmvN45XAoBxT6c_4Dd1IKn5M87bof2Gg?e=hCDMai&CID=BC5CAEB5-1DC1-4A82-B5EF-777BA3EF0CD0&wdLOR=cE38AACAC-3C25-4AE8-9FAF-1D9F5F9435F5
labeling app slides: https://alleninstitute.sharepoint.com/sites/Pika/Shared%20Documents/Forms/AllItems.aspx?id=%2Fsites%2FPika%2FShared%20Documents%2FCell%20Segmentation%202021%2Flabeling%5Fapp%5Finstructions%2Epdf&parent=%2Fsites%2FPika%2FShared%20Documents%2FCell%20Segmentation%202021&p=true&wdLOR=cE503F683%2DCA0C%2D4598%2D8F76%2D295680040A32&ct=1689281348541&or=Outlook%2DBody&cid=F300137C%2D8FC7%2D4A73%2D8A4C%2D4C9C6B7CC5CD&ga=1
Note: this was for the challenging deepscope dataset that had low SNR, but no crosstalk (multiple planes)

Model inputs

matchings commented 1 year ago

Still need to compare this implementation of ROI classification versus other available methods