From Pixels to Patterns: Comprehensive Analysis of Whole Mouse Brain Lightsheet Images

Published: 2024-03-11

Join us for an afternoon of presentations from Euro-BioImaging users and image data/image analysis experts at our Nodes that will provide a compelling overview of the state-of-the-art in Image Data. At the User Forum on Image Data, Euro-BioImaging user, Shiladitya Mitra, explains her image data analysis project undertaken in collaboration with  Michaela Blazikova, IMG, Prague Node. Read the full abstract below.

What: Euro-BioImaging User Forum “Image Data”

When: March 26, 2024, from 14:00-17:00 CEST Where: Online

Full program



From Pixels to Patterns: Comprehensive Analysis of Whole Mouse Brain Lightsheet Images

Shiladitya Mitra, Max Planck Institute of Psychiatry, DE

Michaela Blazikova,

IMG, Prague Node, CZ

Utilizing immunostained and cleared tissue images acquired from a lightsheet microscope, this presentation highlights the pilot Euro-BioImaging image analysis project focused on whole mouse brain plasticity analysis. Brains from three distinct groups of mice were examined to uncover differential c-Fos signaling patterns in various brain regions. The primary objective was to identify variations in c-Fos signal intensity and distribution across different experimental groups using ClearMap, a software tool designed to facilitate cell segmentation in 3D and annotation referencing the Allen Brain Atlas. The analysis pipeline was implemented in Python 3 and made accessible through a Jupyter Notebook environment. Collaboration with the user involved agreement on output specifications and pricing, with an estimated time requirement of 8 hours per individual mouse brain, totaling 96 hours for the entire dataset comprising 12 mouse brains (~100 GB each). The output comprised density maps highlighting brain areas with significant c-Fos signal differences. This post-processing of the results was performed using Matlab. The project was conducted between September 2022 and October 2023, and concluded by sending the final results. Further analyses and exploration of the data were left to the discretion of the user, empowering continued investigation beyond the project's scope. This presentation underscores the efficacy of combining advanced imaging techniques with sophisticated image analysis methodologies and highlights the benefits of outsourcing part of a complex project.

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