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dissection_region_ccf

README.md

cemba_dissection

This repository contains CEMBA dissction region segmentation based on Allen CCFv3 and its average template at 25 micron resolution. This repo provides content to the CEMBA snmC-seq2 data browser

Allen CCFv3

  • See documentation about Allen CCFv3 from the AIBS: https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359
  • To view the dissection segmentation, you need to first unzip the Allen CCFv3 files. All the files downloaded from Allen brain atlas from here, and this paper: Wang, Quanxin, Song-Lin Ding, Yang Li, Josh Royall, David Feng, Phil Lesnar, Nile Graddis, et al. 2020. “The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.” Cell 181 (4): 936–53.e20.
  • Average template NRRD is the background of the segmentation
  • The annotation NRRD is the CCFv3 brain structure segmentation
  • The txt file contain color and label of CCFv3 structures that can be loaded into ITK-SNAP
  • There is a nice documentation in the Allen CCFv3 files (ITK-SNAP_SOP for viewing Tg data and average template.docx) about how to view the CCFv3 files in ITK-SNAP.

ITK-SNAP

Install latest ITK-SNAP to view NRRD files. http://www.itksnap.org/pmwiki/pmwiki.php

CEMBA Dissection Segmentation

  • Both CEMBA_region.nii.gz and CEMBA_region.nrrd.gz are the dissection region segmentations on the CCF's average template.
  • CEMBA_region_anno_itksnap.txt contain color and label of CEMBA dissection regions.
  • As explained in the documentation from Allen CCF (ITK-SNAP_SOP for viewing Tg data and average template.docx), load the average template and CEMBA dissection segmentation in ITK-SNAP to view it or generate mesh.