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 GitHub repository

• 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

Getting started

• Guide on immunofluorescence staining, iDISCO+, & lightsheet fluorescence microscopy

• Installation

• Guide

• unravel package

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

Contents:

• Installation
  • TL;DR on Installation
  • TL;DR on Getting Started
  • Installing UNRAVEL on Linux or WSL
    • Running Linux Applications in WSL
  • Checking UNRAVEL Version Changes
  • Viewing Images:
  • Get Started With Analysis
• Guide
  • Command Help Guides
  • Listing Commands
  • Common Commands
  • Set Up
    • Back Up Raw Data
    • Stitch Z-stacks
    • Make Sample Folders
    • Add Images to sample?? Directories
    • Log Paths, Commands, etc.
    • Make a sample_key.csv:
    • Defining Common Variables for Command Arguments
    • Optional: Clean TIFFs
  • Analysis Overview
  • Training Ilastik
  • Registration
    • io_metadata
    • reg_prep
    • seg_copy_tifs
    • seg_brain_mask
    • reg
    • reg_check
  • Voxel-wise Statistics
    • vstats_prep
    • vstats_z_score
    • utils_agg_files
    • vstats_whole_to_avg
    • vstats
  • Cluster-wise Statistics
    • False Discovery Rate (FDR) Correction
    • cstats_fdr_range
    • cstats_fdr
    • cstats_mirror_indices
  • Segmentation of Full-Resolution Fluorescence Images
    • 1) seg_copy_tifs
    • 2) Train Ilastik to segment c-Fos+ cells or other features
    • 3) seg_ilastik
  • Cluster Validation and Statistics
    • cstats_validation
    • cstats_summary
  • Sunburst Plots
  • 3D Brain Models
  • Valid Cluster Info Tables
  • Region-wise Statistics
    • rstats
    • rstats_summary
  • Example sample?? Folder Structure
  • Example Experiment Folder Structure
• unravel package
  • Subpackages
    • unravel.unravel_commands module
      • Usage to print common commands, aliases, and descriptions:
      • Usage to print all commands matching a specific string:
      • Usage to print all commands and module names:
      • parse_args()
      • main()
    • unravel.register package
      • unravel.register.reg_prep module
      • unravel.register.reg module
      • unravel.register.affine_initializer module
      • unravel.register.reg_check module
      • unravel.register.reg_check_brain_mask module
    • unravel.warp package
      • unravel.warp.to_atlas module
      • unravel.warp.to_fixed module
      • unravel.warp.to_native module
      • unravel.warp.warp module
      • unravel.warp.points_to_atlas module
    • unravel.segment package
      • unravel.segment.brain_mask module
      • unravel.segment.copy_tifs module
      • unravel.segment.ilastik_pixel_classification module
      • unravel.segment.labels_to_masks module
    • unravel.voxel_stats package
      • unravel.voxel_stats.apply_mask module
      • unravel.voxel_stats.vstats_prep module
      • unravel.voxel_stats.z_score module
      • unravel.voxel_stats.whole_to_LR_avg module
      • unravel.voxel_stats.hemi_to_LR_avg module
      • unravel.voxel_stats.vstats module
      • unravel.voxel_stats.mirror module
      • unravel.voxel_stats.other package
    • unravel.cluster_stats package
      • unravel.cluster_stats.fdr_range module
      • unravel.cluster_stats.fdr module
      • unravel.cluster_stats.recursively_mirror_rev_cluster_indices module
      • unravel.cluster_stats.validation module
      • unravel.cluster_stats.summary module
      • unravel.cluster_stats.brain_model module
      • unravel.cluster_stats.find_incongruent_clusters module
      • unravel.cluster_stats.group_bilateral_data module
      • unravel.cluster_stats.mean_IF module
      • unravel.cluster_stats.legend module
      • unravel.cluster_stats.org_data module
      • unravel.cluster_stats.prism module
      • unravel.cluster_stats.cstats module
      • unravel.cluster_stats.stats_table module
      • unravel.cluster_stats.sunburst module
      • unravel.cluster_stats.table module
      • unravel.cluster_stats.crop module
      • unravel.cluster_stats.index module
      • unravel.cluster_stats.mean_IF_summary module
      • unravel.cluster_stats.effect_sizes package
    • unravel.region_stats package
      • unravel.region_stats.rstats module
      • unravel.region_stats.rstats_summary module
      • unravel.region_stats.rstats_mean_IF module
      • unravel.region_stats.rstats_mean_IF_in_segmented_voxels module
      • unravel.region_stats.rstats_mean_IF_summary module
    • unravel.core package
      • unravel.core.help_formatter module
      • unravel.core.config module
      • unravel.core.img_io module
      • unravel.core.img_tools module
      • unravel.core.utils module
    • unravel.image_io package
      • unravel.image_io.h5_to_tifs module
      • unravel.image_io.img_to_npy module
      • unravel.image_io.io_img module
      • unravel.image_io.metadata module
      • unravel.image_io.nii_hd module
      • unravel.image_io.nii_info module
      • unravel.image_io.io_nii module
      • unravel.image_io.nii_to_tifs module
      • unravel.image_io.nii_to_zarr module
      • unravel.image_io.reorient_nii module
      • unravel.image_io.tif_to_tifs module
      • unravel.image_io.zarr_to_nii module
      • unravel.image_io.points_to_img module
      • unravel.image_io.img_to_points module
    • unravel.image_tools package
      • unravel.image_tools.avg module
      • unravel.image_tools.bbox module
      • unravel.image_tools.extend module
      • unravel.image_tools.max module
      • unravel.image_tools.pad module
      • unravel.image_tools.resample module
      • unravel.image_tools.spatial_averaging module
      • unravel.image_tools.DoG module
      • unravel.image_tools.rb module
      • unravel.image_tools.transpose_axes module
      • unravel.image_tools.unique_intensities module
      • unravel.image_tools.resample_points module
      • unravel.image_tools.atlas package
    • unravel.utilities package
      • unravel.utilities.get_samples module
      • unravel.utilities.aggregate_files_from_sample_dirs module
      • unravel.utilities.aggregate_files_recursively module
      • unravel.utilities.clean_tif_dirs module
      • unravel.utilities.prepend_conditions module
      • unravel.utilities.rename module
      • unravel.utilities.toggle_samples module
      • unravel.utilities.points_compressor module
  • Module contents

Indices

• Index

• Module Index

• Search Page