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Updated: May 20, 2026

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy
Published on: August 1, 2022
Biological imaging software tools
Kevin W Eliceiri1, Michael R Berthold, Ilya G Goldberg
1Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA. eliceiri@wisc.edu
Abstract:
Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics, focusing on open-source options.
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