ArticleNature communications2021
Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
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Who cites it
56 citing papers in PubMed.
- Accelerated immunostaining of thick biological tissues using bidirectional electric fields with reversible deformation.Biomedical optics express · 2026Article
- Fluorescent Labeling Methods for Brain Structure Research.Molecules (Basel, Switzerland) · 2026Review
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- mViSE: A visual search engine for analyzing multiplex IHC brain tissue images (spatial proteomics).Scientific reports · 2026Article
- Weak-to-strong generalization enables fully automated training of multi-head mask-RCNN model for segmenting densely overlapping cell nuclei in multiplex whole-slice brain images.Frontiers in bioinformatics · 2026Article
- Longitudinal human transcriptomic and spatial gene profiling at the incisional edge during long surgical procedures.Communications biology · 2025Article
- Chemoarchitectural studies of the rat hypothalamus and zona incerta.bioRxiv : the preprint server for biology · 2025Article
- Antibody-Based Multiplex Image Analysis: Standard Analytical Workflows and Artificial Intelligence Tools for Pathologists.Laboratory investigation; a journal of technical methods and pathology · 2025Review
- From Biomarkers to Behavior: Mapping the Neuroimmune Web of Pain, Mood, and Memory.Biomedicines · 2025Article
- Mass Spectrometry Imaging.Analytical chemistry · 2025Review
- Quantitative benchmarking of nuclear segmentation algorithms in multiplexed immunofluorescence imaging for translational studies.Communications biology · 2025Article
- Huntingtin inclusion bodies have distinct immunophenotypes and ubiquitination profiles in the Huntington's disease human cerebral cortex.Scientific reports · 2025Article
- Efficient removal of naturally-occurring lipofuscin autofluorescence in human nervous tissue using high-intensity white light.The journal of pain · 2025Article
- Characterization of theFASEB bioAdvances · 2025Article
- A Combination of Low Doses of Lithium and Valproate Improves Cognitive Outcomes after Mild Traumatic Brain Injury.Journal of neurotrauma · 2025Article
- Robust collection and processing for label-free single voxel proteomics.Nature communications · 2025Article
- Laser capture microdissection.Nature reviews. Methods primers · 2025Article
- Age-dependent integration of cortical progenitors transplanted at CSF-neurogenic niche interface.Frontiers in cell and developmental biology · 2025Article
- The μ-opioid receptor differentiates two distinct human nociceptive populations relevant to clinical pain.Cell reports. Medicine · 2024Article
- Hippocampal aggregation signatures of pathogenic UBQLN2 in amyotrophic lateral sclerosis and frontotemporal dementia.Brain : a journal of neurology · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.