Description:

heifetslabunravel 1.0.0b9

UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images

UNRAVEL is a Python package & command line tool for the analysis of brain-wide imaging data, automating:

Registration of brain-wide images to a common atlas space
Quantification of cell/label densities across the brain
Voxel-wise analysis of fluorescent signals and cluster correction
Validation of hot/cold spots via cell/label density quantification at cellular resolution


UNRAVEL can be installed via PyPI: pip install heifetslab-unravel
Initial UNRAVEL publication
UNRAVEL was developed by the Heifets lab and TensorAnalytics
Additional support/guidance was provided by:

The Shamloo lab
The Malenka lab
The Stanford-based P50 center funded by NIDA




Please see UNRAVEL documentation for guides on installation and analysis


UNRAVEL visualizer

UNRAVEL visualizer is a web-based tool for visualizing and exploring 3D maps output from UNRAVEL
UNRAVEL visualizer GitHub repo
Developed by MetaCell with support from the Heifets lab


Contact us
If you have any questions, suggestions, or are interested in collaborations and contributions, please reach out to us.
Developers

Daniel Ryskamp Rijsketic (developer and maintainer) - danrijs@stanford.edu
Austen Casey (developer) - abcasey@stanford.edu
MetaCell (UNRAVEL visualizer developers) - info@metacell.us
Boris Heifets (PI) - bheifets@stanford.edu

Additional contributions from

Mehrdad Shamloo (PI) - shamloo@stanford.edu
Daniel Barbosa (early contributer and guidance) - Dbarbosa@pennmedicine.upenn.edu
Wesley Zhao (guidance) - weszhao@stanford.edu
Nick Gregory (guidance) - ngregory@stanford.edu

Main dependencies

Allen Institute for Brain Science
FSL
fslpy
ANTsPy
Ilastik
nibabel
numpy
scipy
pandas
cc3d
Registration and warping workflows were inspired by MIRACL
We warped this LSFM/iDISCO+ average template brain to Allen brain atlas space (CCFv3) and refined alignment.

Support is welcome for

Analysis of new datasets
Development of new features
Maintenance of the codebase
Guidance of new users

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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