CaImAn

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This changes the naming semantics (slightly) and parsing of memmap files to make them less fragile to oddly-named input files and to make them easier to read/maintain. It has the...

pgunn

caimanmanager.py install fail

18

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...

kas5dv

Issue saving `cnn_preds` when CNMF params tuned for dendrites

1

- **Tell us a bit about your setup**: 1. Operating system (Linux/macOS/Windows): Linux, Debian 2. Python version (3.x): 3.10 3. Working environment (Python IDE/Jupyter Notebook/other): Jupyter notebook 4. Which of...

kushalkolar

Suggestion: remove SBX loading code and recommend using sbxreader instead

23

### Discussed in https://github.com/flatironinstitute/CaImAn/discussions/1298 Originally posted by **ethanbb** March 14, 2024 Hello, This is mainly a documentation suggestion. My microscope saves Scanbox files, and I saw CaImAn has support for...

EricThomson

Fix problem with using reloaded cnmf object

2

# Description Issue raised with using reloaded data, the way things are serialized with hdf5, they are loaded as byte-encoded, so when you try to change parameters things don't work...

EricThomson

Handle warnings about upcoming deprecations

1

Turned off warnings and checked for upcoming deprecations. Most of these are repeated many times in the different notebooks, just noting the warnings not where they are occurring in the...

EricThomson

# Description Handles some minor upcoming deprecations as discussed in issue: Closes #1303 # Type of change - [X] Bug fix (non-breaking change which fixes an issue) ## Testing Tested...

EricThomson

fix bug in correlation image calculation

1

# Description Fixes bug pointed out by @rcalfredson and implements fix suggested by @j-friedrich in discussion #1190 # Type of change - [X] Bug fix (non-breaking change which fixes an...

EricThomson

# Caiman Roadmap: August 2023 - August 2024 Our goals with Caiman naturally fall into three general categories: - **Usability** – make Caiman's current feature base easier to use. -...

EricThomson

Better error when using data with less than 200 frames for mcorr

3

Instead of current numpy indexerror

kushalkolar