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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
Follow these instructions (https://int-brain-lab.github.io/iblenv/one_docs/one_credentials.html#using-the-one-setup-method) to set up a JSON parameter file (named .one_params). The only field that you may want to change is the CACHE_DIR (this is where the GUI will look for the Allen Atlas files (see step 3)). All other fields should be kept as the default by pressing enter when prompted.
Download the Allen Brain Atlas templates annotation_25.nrrd and average_template_25.nrrd templates from the following links
- http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/
- http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/average_template/
Places these files in a folder in the following path on your computer
CACHE_DIR/histology/ATLAS/Needles/Allen
where the CACHE_DIR is the path you entered in step 2
Please refer to the section Preparing data for ephys GUI section 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 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.