suite2p
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MouseLand
cell detection in calcium imaging recordings
I had a frustrating time dealing with the bugs and default behavior of the merge process so here are some proposed changes. My use case is that I am imaging...
In response to https://github.com/MouseLand/suite2p/issues/747 This is my first contribution - please let me know if there is anything I could improve!
Tested this version against the base repo in a different virtual environment and saw no differences in the GUI or how it visualizes ROIs
Added keyboard shortcut to change from red cell to not red cell by pressing C in the GUI. Added function `flip_redcell` to masks.py which implements the change, which is called...
This PR does the following: - Save `F_chan2` and `Fneu_chan2` to NWB (fixes https://github.com/MouseLand/suite2p/issues/817), - Add planes fluorescence containers to NWB, - Separate ROIs for each plane in NWB, -...
Hi, I am running suite2p v0.11.0 on12-plane datasets, using `anatomical_only = 3` for ROI detection. I noticed that the process crashes when no ROI is detected at a plane. e.g....
I updated my s2p to the main github branch. When trying to process a stack, I ran into a memory error when using torch.ifft ( DefaultCPUAllocator: not enough memory: you...
I'm processing my data on a machine with Ubuntu, and then add manually some cells later on, on a different machine (macOS). Everything works well except when I try do...
I'm working with a team that has mesoscope data with 4 ROIs across 2 planes, recorded over time, and fixed z-depths. So far, images have been processed by splitting `tifs`...
My understanding is that with anatomical (cellpose) mode, only the time-averaged fluorescence is used for cell detection, i.e. activity does not play a role in finding cells. Is that accurate?...
