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1. Installation
Follow these instructions https://github.com/int-brain-lab/iblenv to install a unified environment that is compatible with all IBL libraries being developed
Follow these instructions to configure ONE and Datajoint credentials that give automatic access to IBL data
- https://int-brain-lab.github.io/iblenv/one_docs/one_credentials.html
- https://int-brain-lab.github.io/iblenv/dj_docs/dj_credentials.html
The ephys alignment gui can be launched from a python terminal using the following commands
conda activate iblenv
# path to the ephys_atlas_gui.py file on your computer
python int-brain-lab\iblapps\atlaselectrophysiology\ephys_atlas_gui.py
A window containing blank plots should appear. Please refer to the Usage instructions for how to load data and start using the GUI.
In order to create the unified environment for using IBL repositories, first download and install Anaconda and git, and follow their installer instructions to add each to the system path. Also, please ensure Anaconda is installed to your home directory. The below instructions will tell you how to set up and activate the unified conda environment (iblenv) and properly install multiple repositories within this environment.
In your git terminal, navigate to the directory in which you want to install the IBL repositories (e.g. create a folder named something like int-brain-lab and work from within it). Then run the following commands:
conda update -n base -c defaults conda
conda create --name iblenv python=3.10 --yes
git clone https://github.com/int-brain-lab/iblapps
pip install --editable iblapps
Please refer to the section Preparing data for ephys GUI for instructions of how to prepare your data in the correct format to be read in by the GUI
We have also provided a sample data set so you can quickly get started and try out the tool. The data is stored in the ephys_alignment_sample_data.zip folder and can be downloaded from here
The ephys alignment GUI can be launched from a python terminal using the following commands
conda activate iblenv
# path to the ephys_atlas_gui.py file on your computer
python int-brain-lab\iblapps\atlaselectrophysiology\ephys_atlas_gui.py -o True
The -o True argument is important to indicate that you are using the alignment GUI in non IBL mode
A window containing blank plots should appear. Please refer to the Usage instructions for how to load data and start using the GUI.
N.B. Some mac users using Big Sur OS have reported that the window does not appear upon executing the command above. If this is the case please refer to this section for a workaround