Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks.
Dragan MaricJahandar JahanipourXiaoyang Rebecca LiAditi SinghAryan MobinyHien Van NguyenAndrea SedlockKedar GramaBadrinath RoysamPublished in: Nature communications (2021)
Mapping biological processes in brain tissues requires piecing together numerous histological observations of multiple tissue samples. We present a direct method that generates readouts for a comprehensive panel of biomarkers from serial whole-brain slices, characterizing all major brain cell types, at scales ranging from subcellular compartments, individual cells, local multi-cellular niches, to whole-brain regions from each slice. We use iterative cycles of optimized 10-plex immunostaining with 10-color epifluorescence imaging to accumulate highly enriched image datasets from individual whole-brain slices, from which seamless signal-corrected mosaics are reconstructed. Specific fluorescent signals of interest are isolated computationally, rejecting autofluorescence, imaging noise, cross-channel bleed-through, and cross-labeling. Reliable large-scale cell detection and segmentation are achieved using deep neural networks. Cell phenotyping is performed by analyzing unique biomarker combinations over appropriate subcellular compartments. This approach can accelerate pre-clinical drug evaluation and system-level brain histology studies by simultaneously profiling multiple biological processes in their native anatomical context.
Keyphrases
- resting state
- white matter
- high resolution
- single cell
- neural network
- functional connectivity
- cerebral ischemia
- cell therapy
- emergency department
- gene expression
- deep learning
- mesenchymal stem cells
- magnetic resonance imaging
- oxidative stress
- computed tomography
- photodynamic therapy
- cell death
- magnetic resonance
- air pollution
- high throughput
- endoplasmic reticulum stress