https://github.com/aswendt-lab/aidahisto
Atlas-based imaging data analysis tool for quantitative mouse brain histology (AIDAhisto)
Science Score: 36.0%
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Repository
Atlas-based imaging data analysis tool for quantitative mouse brain histology (AIDAhisto)
Basic Info
Statistics
- Stars: 4
- Watchers: 0
- Forks: 2
- Open Issues: 0
- Releases: 3
Metadata Files
README.md
AIDAhisto
Atlas-based imaging data analysis tool for quantitative mouse brain histologySoftware to automatically detect cells in histological mouse brain and spinal cord sections. Tested for different immunostainings (e.g., GFAP, Iba1, and MAP2) and histological stainings (e.g., Nissl). The Allen Mouse Brain/Spinal Cord Atlas is used to register the microscopy files. Cell counting results are reported as cells per brain region.
Information about Version 1.2 (current) / Version 1.1 / Version 1.0
EXAMPLES
FEATURES
Please note that we stopped supporting Python-based tools. All corresponding tools are available for Matlab.Includes a custom version of the Allen Mouse Brain/Spinal Cord Atlas with a list of annotations
Instruction on how to register the atlas with microscopy files using ImageJ
Automated cell counting
Cell counting works for immunostainings and histological stainings; the cell nuclei position (e.g. based on a DAPI staining) can be used to improve the cell counting (only cells with a cell nuclei will be counted)
GET STARTED
Download the modified atlas files and the test images (including representative results) here. For details on installation and use, see the step-by-step guide in the Manual v1.2.
CITATION
When applying or modifying AIDAhisto, please always cite the original reference: Pallast, N., et al. "Atlas-based imaging data analysis tool for quantitative mouse brain histology (AIDAhisto)" Journal of Neuroscience Methods, 2019
CONTACT
Chat with us [
or
join our Open Office Hour - each Thursday 3:00 pm (UTC+2)
Markus Aswendt (markus.aswendt@uk-koeln.de)
LICENSE
CC BY-NC-SA 4.0
REFERENCES
- Allen Institute for Brain Science (2004). Allen Mouse Brain Atlas and Allen Mouse Spinal Cord Atlas. Available from mouse.brain-map.org. Allen Institute for Brain Science (2011). Source: Allen Mouse Brain Atlas, Allen Mouse Spinal Cord Atlas
- Allen Brain Reference Atlas: Lein, E.S. et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain, Nature 445: 168-176. , Harris, J. A. et al. (2019). Hierarchical organization of cortical and thalamic connectivity. Nature 575, 195-202, Oh, Seung Wook, et al. "A mesoscale connectome of the mouse brain." Nature, 2014
- AIDAhisto Pallast, N., et al. "Atlas-based imaging data analysis tool for quantitative mouse brain histology (AIDAhisto)" Journal of Neuroscience Methods, 2019
- AIDAmri Pallast, N., et al. "Processing pipeline for Atlas-based Imaging Data Analysis (AIDA) of structural and functional mouse brain MRI" Frontiers in Neuroinformatics, 2019
- Incremental cell search Meruvia-Pastor, Oscar E., et al. "Estimating cell count and distribution in labeled histological samples using incremental cell search" Journal of Biomedical Imaging, 2011
Owner
- Name: Aswendt-Lab
- Login: Aswendt-Lab
- Kind: organization
- Location: Germany
- Repositories: 3
- Profile: https://github.com/Aswendt-Lab