ArticleeNeuro
A Semi-Automated Workflow for Brain Slice Histology Alignment, Registration, and Cell Quantification (SHARCQ).
Article in eNeuro. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 26 citations in OpenAlex.
- Spatial transcriptomics reveals distinct cell type dynamics following opioid dependence in female mice with the common human μ-opioid receptor variant Oprm1 A118G.Nature communications · 2026Article
- GABAergic projections from the suprachiasmatic nucleus to the preoptic area regulate the timing of torpor in mice.Nature communications · 2026Article
- Central amygdalar PKCδ neurons mediate fentanyl withdrawal.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping in different species.Cell reports methods · 2026Article
- LFP-LOC: an LFP power-based method for validating the anatomical placement of high-density neural probes in rodents.Frontiers in neuroscience · 2026Article
- Article
- VTA µ-Opioidergic Neurons Facilitate Low Sociability in Protracted Opioid Abstinence.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Bell Jar: A Semiautomated Registration and Cell Counting Tool for Mouse Neurohistology Analysis.eNeuro · 2025Article
- Software and pipelines for registration and analyses of rodent brain image data in reference atlas space.Frontiers in neuroinformatics · 2025Article
- Early synaptic dysfunction of striatal parvalbumin interneurons in a mouse model of Parkinson's disease.iScience · 2024Article
- Monosynaptic Inputs to Ventral Tegmental Area Glutamate and GABA Co-transmitting Neurons.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Article
- Defining spatial nonuniformities of all ipRGC types using an improved Opn4Cell reports methods · 2024Article
- Retrosplenial inputs drive visual representations in the medial entorhinal cortex.Cell reports · 2024Article
- VTA μ-opioidergic neurons facilitate low sociability in protracted opioid withdrawal.bioRxiv : the preprint server for biology · 2024Article
- A newbioRxiv : the preprint server for biology · 2024Article
- Ventral tegmental area glutamate neurons establish a mu-opioid receptor gated circuit to mesolimbic dopamine neurons and regulate opioid-seeking behavior.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2023Article
- Retrosplenial inputs drive diverse visual representations in the medial entorhinal cortex.bioRxiv : the preprint server for biology · 2023Article
- Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model.bioRxiv : the preprint server for biology · 2023Article
- Evaluation of cellular activity in response to sleep deprivation by a comprehensive analysis of the whole mouse brain.Frontiers in neuroscience · 2023Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Tools for refined cell-specific targeting have significantly contributed to understanding the characteristics and dynamics of distinct cellular populations by brain region. While advanced cell-labeling methods have accelerated the field of neuroscience, specifically in brain mapping, there remains a need to quantify and analyze the data. Here, by modifying a toolkit that localizes electrodes to brain regions (SHARP-Track; Slice Histology Alignment, Registration, and Probe-Track analysis), we introduce a post-imaging analysis tool to map histological images to established mouse brain atlases called SHARCQ (Slice Histology Alignment, Registration, and Cell Quantification). The program requires MATLAB, histological images, and either a manual or automatic cell count of the unprocessed images. SHARCQ simplifies the post-imaging analysis pipeline with a step-by-step GUI. We demonstrate that SHARCQ can be applied for a variety of mouse brain images, regardless of histology technique. In addition, SHARCQ rectifies discrepancies in mouse brain region borders between atlases by allowing the user to select between the Allen Brain Atlas or the digitized and modified Franklin-Paxinos Atlas for quantifying cell counts by region. SHARCQ produces quantitative and qualitative data, including counts of brain-wide region populations and a 3D model of registered cells within the atlas space. In summary, SHARCQ was designed as a neuroscience post-imaging analysis tool for cell-to-brain registration and quantification with a simple, accessible interface. All code is open-source and available for download (https://github.com/wildrootlab/SHARCQ).
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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.