Installation

Manual

mkdir -p ~/src
cd ~/src

# My modified version of suite2p
git clone https://github.com/tom-f-oconnell/suite2p

git clone https://github.com/ejhonglab/hong2p
git clone https://github.com/ejhonglab/al_analysis

# This will make a conda environment named 'suite2p'
conda env create -f suite2p/environment.yml

conda activate suite2p
cd ~/src/al_analysis
pip install -r requirements.txt

Then set the environment variables HONG_NAS and HONG2P_FAST_DATA appropriately:

• $HONG_NAS should contain a directory mb_team directly under it.

  • This mb_team directory should contain raw_data and stimulus_data_files directly under it.

  • You may also set HONG2P_DATA as a folder that contains raw_data and stimulus_data_files directly under it.

• $HONG2P_FAST_DATA should contain a local copy of the data under a raw_data directory, again immediately under it. Analysis intermediates will be saved to a directory analysis_intermediates, which will be created under this directory.

Mostly automated

To install as manual install above, but using SSH authentication, you may simply call ./install.sh after cloning. If it asks you to set environment variables, you will need to manually do so.

Setting up link to Google sheet with metadata

For the analysis to use the metadata in my Google Sheet Hong lab documents/Tom - odor mixture experiments/pair_grid_data, open the sheet and copy the link to a file called pair_grid_data_gsheet_link.txt in the top-level of this repository.

Running

# (or whatever else you named the environment for this project)
conda activate suite2p

./al_analysis.py

Plots will be created under a directory such as svg, under the current directory.

Installation notes

Only tested on Ubuntu 18.04.

Note that despite the fact that suite2p/environment.yml includes the line suite2p, my current conda installation (despite conda clean -a and deleting all but the base environment) thinks it already has suite2p when it gets to that part of the install step. This is only really an issue because it suggests some other dependencies may not be installed correctly, as I would otherwise want to prevent suite2p from being installed, so that I can install an editable version of my fork without any ambiguity about other versions possibly being installed.

This is the relevant line:

Requirement already satisfied: suite2p in /home/tom/src/suite2p (from -r /home/tom/src/suite2p/      condaenv.npju4l22.requirements.txt (line 15)) (0.10.2.dev11+gc7af998.d20210802)