Software 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
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Includes a custom version of the Allen Mouse Brain/Spinal Cord Atlas with a list of annotations
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Instruction on how to register the atlas with microscopy files using ImageJ
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Automated cell counting
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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)
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.
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
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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