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Updated: Apr 17, 2026
Quantifying Microglia Morphology from Photomicrographs of Immunohistochemistry Prepared Tissue Using ImageJ
Published on: June 5, 2018
Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors
Murad Megjhani1, Nicolas Rey-Villamizar1, Amine Merouane1
1Department of Electrical and Computer Engineering, University of Houston, Houston, TX, USA, Center for Integrative Brain Research, Seattle Children's Hospital, Seattle, WA 98101, USA and Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
This study introduces a new automated method for reconstructing and analyzing 3D microglial arbors in brain tissue. The scalable algorithm accurately maps microglia activation states, improving cell analysis in neuroscience research.
Area of Science:
- Neuroscience
- Computational Biology
- Microscopy
Background:
- Microglial arbor morphology is a key indicator of brain cell activation.
- Accurate and scalable methods are needed to reconstruct 3D microglial arbors and map activation states in large brain tissue regions.
Purpose of the Study:
- To develop and validate an automated, robust, and scalable method for reconstructing 3D microglial arbors.
- To quantitatively map microglia activation states across extended brain tissue areas.
Main Methods:
- Multiplex immunolabeling of thick rat brain sections (IBA1, Hoechst).
- Confocal microscopy with automated 3D image mosaicing for large-scale imaging.
- An over-complete dictionary-based model and a scalable algorithm for seamless microglial arbor reconstruction.
- Quantification of arbor morphology using L-measure and classification of activation states via harmonic co-clustering.
Main Results:
- The automated method achieved higher accuracy and fewer spurious points compared to existing vesselness and LoG-based methods.
- Four distinct microglial morphology classes were identified, correlating with known activation patterns.
- Spatial distributions of microglial activation and cell abundances were successfully mapped.
Conclusions:
- The developed method provides accurate, scalable, and robust reconstruction of 3D microglial arbors.
- This approach enables quantitative mapping of microglia activation states over large brain tissue volumes.
- The open-source software and protocols facilitate broader application in neuroscience research.
