heifetslab-unravel 1.0.0b14

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