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

• 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)

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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Markus Aswendt ([email protected])

LICENSE CC BY-NC-SA 4.0