CaImAn

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Analysis inside a region designated by a Binary Mask

2

Please fill in the following for any issues Your setup: 1. Operating System (Linux, MacOS, Windows): MacOS 2. Hardware type (x86, ARM..) and RAM: M1 16 gb 3. Python Version...

ggmirandac

reconstruct the movie according to ROIs

3

Hello! I wonder, can I reconstruct the movie based on the components I am interested in? For example, 1) I tried different parameters and found there are differences between each...

zhouyi0812

evaluate_components crashes when using non-integer gSig

6

I don't know if there is a strong reason to use integers for the values of gSig, but I tried using [2.5, 2.5] and CNMF ran just fine. However, when...

oterocoronel

Would be nice to add ability to save motion correction object the way Caiman already saves the CNMF object. Motion correction can take a *really* long time, and it would...

EricThomson

openCV issue when playing the movie

21

Hello! I ran the demo pipeline on a test imaging session that I took (single tiff, 3.8GB). I can successfully go through all the steps, except when trying to display...

andrestrocyte

all these correlation functions

3

There are _a lot_ of correlation functions in `caiman.summary_images` and it's not easy to understand them from the names and docstrings. I think it would be important to make a...

kushalkolar

Design Discussion: Execution Context

5

Idea: Replace dview with an object that I'm initially calling an Execution Context, a class that holds the following information: * The type of parallelism used for a run, stored...

pgunn

Out of memory with demo_pipeline_cnmfE.py

9

For better support, please use the template below to submit your issue. When your issue gets resolved please remember to close it. Sometimes errors while running CNMF occur during parallel...

restrepd

Right now it's a bit involved to take neurons that have been externally detected and bring them into Caiman. We have a notebook to do it, but it needs some...

pgunn

Tracking issue: Investigate alternatives to z5py

1

Right now z5py is a dynamic import because it's only available on conda-forge. This is less than ideal (we don't want any new dynamic imports, and it'd be great to...

pgunn