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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.
First start by installing the latest version of Anaconda 64 bit and Git if not already installed
In an anaconda prompt type the following commands
mkdir int-brain-lab
cd int-brain-lab
git clone https://github.com/int-brain-lab/ibllib.git --branch develop ibllib-repo
git clone https://github.com/int-brain-lab/iblapps.git --branch develop
git clone https://github.com/int-brain-lab/iblenv.git
git clone https://github.com/cortex-lab/phylib
conda env create -f ./iblenv/iblenv.yaml
conda activate iblenv
conda develop ./ibllib-repo
conda develop ./iblapps
conda develop ./phylib
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.