The Active Atlas: Combining 3D Anatomical Models with Texture Detectors

Chen, Yuncong, McElvain, Lauren, Tolpygo, Alex, Ferrante, Daniel, Karten, Harvey, Mitra, Partha, Kleinfeld, David, Freund, Yoav (February 2017) The Active Atlas: Combining 3D Anatomical Models with Texture Detectors. arXiv. (Submitted)

[thumbnail of 1702.08606v3.pdf] PDF
1702.08606v3.pdf - Submitted Version
Available under License Creative Commons Attribution Non-commercial.

Download (3MB)
DOI: 10.48550/arXiv.1702.08606


While modern imaging technologies such as fMRI have opened exciting new possibilities for studying the brain in vivo, histological sections remain the best way to study the anatomy of the brain at the level of single neurons. The histological atlas changed little since 1909 and localizing brain regions is a still a labor intensive process performed only by experienced neuro-anatomists. Existing digital atlases such as the Allen Brain atlas are limited to low resolution images which cannot identify the detailed structure of the neurons. We have developed a digital atlas methodology that combines information about the 3D organization of the brain and the detailed texture of neurons in different structures. Using the methodology we developed an atlas for the mouse brainstem and mid-brain, two regions for which there are currently no good atlases. Our atlas is "active" in that it can be used to automatically align a histological stack to the atlas, thus reducing the work of the neuroanatomist.

Item Type: Paper
Subjects: Investigative techniques and equipment > brain atlas
organism description > animal > mammal > rodent > mouse
neurobiology > neuroanatomy
CSHL Authors:
Communities: CSHL labs > Mitra lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 27 February 2017
Date Deposited: 13 Oct 2023 16:06
Last Modified: 02 Jan 2024 15:25
Related URLs:

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving