caiman-napari-prototype

Prototype caiman plugin for the napari viewer.

mesmerize-napari

This was a prototype, please see mesmerize-napari.

CNMF demo

This plugin interfaces with CaImAn CNMF using QProcess and displays the spatial components using napari.layers.shapes. stdout from the ongoing QProcess is shown in the text area on the right.

Streaming demo

Napari can stream calcium imaging movies in realtime while pyqtgraph is used to show calcium traces. Please note that due to limitations of GIF images, this GIF doesn't fully represent the high level of responsiveness and interactivity during live streaming.

Creating a working environment

The installation of napari and caiman in the same env is a work in progress. This order of steps worked for me on Ubuntu.

Install napari first and then caiman

Clone napari, install requirements, and install in editable mode:

git clone https://github.com/napari/napari.git
cd napari
pip install -r requirements.txt
pip install -e ".[all]"

Install caiman from my fork (dependency issues related to the latest versions of h5py and tensorflow, should probably make a PR after figuring it out):

git clone https://github.com/kushalkolar/CaImAn.git
cd CaImAn
pip install -r requirements.txt

You will see the following dependency issues after the installation:

hdmf 2.5.8 requires h5py<3,>=2.9, but you'll have h5py 3.3.0 which is incompatible.
hdmf 2.5.8 requires numpy<1.21,>=1.16, but you'll have numpy 1.21.0 which is incompatible.
pynwb 1.5.1 requires h5py<3,>=2.9, but you'll have h5py 3.3.0 which is incompatible.
pynwb 1.5.1 requires numpy<1.21,>=1.16, but you'll have numpy 1.21.0 which is incompatible.
networkx 2.5.1 requires decorator<5,>=4.3, but you'll have decorator 5.0.9 which is incompatible.
tensorflow 2.4.2 requires h5py~=2.10.0, but you'll have h5py 3.3.0 which is incompatible.
tensorflow 2.4.2 requires numpy~=1.19.2, but you'll have numpy 1.21.0 which is incompatible.
tensorflow 2.4.2 requires six~=1.15.0, but you'll have six 1.16.0 which is incompatible.
tensorflow 2.4.2 requires typing-extensions~=3.7.4, but you'll have typing-extensions 3.10.0.0 which is incompatible.

Installing tensorflow~=2.4.0 again after the previous step seems to downgrade numpy and the other things to the right version

The latest version of holoview is also giving issues with panel, using holoviews~=1.12.0 allows caiman to import but just produces a massive warning