This repository contains metadata files for cell migration datasets curated, or in the process of being curated, by the Cell Migration Standardisation Organisation (CMSO).
Each folder represents a given dataset and has a unique accession number. Within each folder, the top-level README describes the dataset linking to the reference publication if available, it indicates the level of curation performed and what metadata files are included.
After the curation is performed, the expected metadata files represent the three units of information defined by CMSO:
- the experimental setup, expressed using the ISA format
- the imaging metadata, expressed via OME companion files
- the tracking data, expressed using the CMSO Biotracks format
In order to submit a new dataset, a minimal set of information needs to be provided based on the MIACME guidelines.
We welcome issues in the tracker as well as Pull Requests suggesting changes to the datasets available in this repository.
If you would like to run locally the dataset validation code from this repository, you can follow the following steps:
- Clone the repository
git clone https://github.com/CellMigStandOrg/CMSO-datasets - We suggest you use a python virtual environment. So, if not already installed in your system, first install the virtual environment via
pip:pip install virtualenv - Create a virtual environment:
virtualenv venv - Then, activate the virtual environment:
source venv/bin/activate - Install the requirements:
pip install -r requirements.txt - Validate the ISA metadata:
python check_isa.py - Validate the biotracks datapackage:
python check_dpkg.py