CaImAn

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Running volpy on linescans

1

Hello, I am using Linux with Python 3.8.8 on Spyder 4.2.5. I installed CaImAn (version 1.9.2) using the pip install -e . method. I'm interested in using the demo_pipeline_voltage_imaging.py script,...

m-bellv

For better support, please use the template below to submit your issue. When your issue gets resolved please remember to close it. - **Tell us a bit about your setup**:...

agiovann

cannot import name 'file_hash' from 'pooch.utils'

2

- **Tell us a bit about your setup**: 1. Operating system (Linux/macOS/Windows): Ubuntu 20.04.3 LTS 2. Python version (3.x): 3.9 3. Working environment (Python IDE/Jupyter Notebook/other): Jupyter Lab 5. CaImAn...

obarnstedt

Large number of non-neuron spatial footprints

8

- **Tell us a bit about your setup**: 1. Operating system (Linux/macOS/Windows): Ubuntu Linux 19.04 2. Python version (3.x): 3.7 3. Working environment (Python IDE/Jupyter Notebook/other): Jupyter Notebook 4. Which...

jchutrue

Shape and size of detected cells using quality parameters

3

In order to tune the shape around the cell, that is the cell boundaries, i believe one has to tune the quality parameters below: ``` cnm.params.set('quality', {'SNR_lowest': 0.7, 'min_SNR': 6,...

akatav

Improvement: add HajiRassouliha et al 2017 algorithm as an alternative to Guizar-Sicairos for motion correction

3

A recent publication by HajiRassouliha et al (HajiRassouliha, A., Taberner, A. J., Nash, M. P., & Nielsen, P. M. F. (2017). Subpixel phase-based image registration using Savitzky-Golay differentiators in gradient-correlation....

michaelfsp

NWB: save motion-corrected data

7

Looks like an initial attempt was made to save a [CorrectedImageStack](https://pynwb.readthedocs.io/en/stable/pynwb.ophys.html#pynwb.ophys.CorrectedImageStack) according to NWB schema. It'd be great to have this feature! Especially as the current `mmap` serialization will fail...

tbenst

cnmf.fit: support npy/NWB/hdf5

14

- **Describe the issue that you are experiencing** When calling `cnmf.fit`, this line loads the entire dataset into memory: https://github.com/flatironinstitute/CaImAn/blob/89ea84845d56f75f29f411c53c046e7fa0c79e9a/caiman/source_extraction/cnmf/cnmf.py#L451 One other line below this would likely cause the same...

tbenst

support for in-memory movies with patch mode?

3

I would like to use the CNMF object in patch mode, but with a matrix Y that is in-memory, and not from a memmapped file. However when I try this,...

mschachter

VolPy Mask_RCNN does not work in CaImAn 1.9.9 or later

4

- **Tell us a bit about your setup**: 1. Linux CentOS7 2. Python 3.9.13, cuda 11, Tesla V100 3. Jupyter Lab (remote) 4. [demo_pipeline_voltage_imaging.py] 5. CaImAn version : 1.9.9 or...

KawashimaLab