Installation

git clone --recurse-submodules git@github.com:alihaydaroglu/s2p-lbm.git
conda env create -f environment.yml
conda activate s2p-lbm
cd suite2p
pip install -e .

If installation gets stuck around "Solving Environment", you should use libmamba (explanation), install it using the instructions here. Also, set the conda channel priority to be strict: conda config --set channel_priority strict. It's important that you don't forget the -e in the pip command, this allows the suite2p installation to be editable.

Updating

Everytime you do git pull, you should also do git submodule update to pull the latest version of my suite2p branch, which is a submodule of this repo. If you find this annoying, you can make git do it automatically

Usage

Run a jupyter notebook in this envinronment, either by running jupyter notebook in the suite3d-gpu conda environment or running a jupyter server from a different conda env and selecting this environment for the kernel (see here). Make sure you use the correct environment!

Then, run the Demo notebook.

UI only installation

If you want to only visualize results on your local laptop, you can install a lightweight script that doesn't have any of the computational dependencies.

git clone --recurse-submodules git@github.com:alihaydaroglu/s2p-lbm.git
conda create -y -n s3d-vis -c conda-forge python=3.9
conda activate s3d-vis
pip install "napari[pyqt5]"
pip install notebook
conda install pyqtgraph
conda install -c conda-forge matplotlib

Docker

There is a Dockerfile in this repo that successfully builds (docker build - < Dockerfile). I don't know anything about Docker, but I would love to have this successfully run in a container. If you manage to get that working let me know! Ideally, this would also include some sort of X host to run napari (https://napari.org/stable/howtos/docker.html#base-napari-image), presumably there is a way to merge the napari-xpra docker image into this one to make that work.

Sample Data

Demo data can be found here: https://liveuclac-my.sharepoint.com/:f:/g/personal/ucqfhay_ucl_ac_uk/EqCoF5CmM1hFvkaj2aPPpcMByfP2j_dzRT8u84S6VT1vKQ?e=EhAgH5 - the password is the name of this repository, all lowercase. You will also find a "results" directory here that should be similar to the exported results if you run this on your computer - you can download this to test the UI component only.