ArticleeLife2023
Histological E-data Registration in rodent Brain Spaces.
Article in eLife, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 20 citations in OpenAlex.
- Thalamocortical bursts encode reward contingencies and drive associative learning.Nature communications · 2026Article
- Induction of cortical on/off periods in awake mice fulfills sleep functions.Nature neuroscience · 2026Article
- Article
- Large-scale electrophysiology at single-spike resolution.Nature reviews. Neuroscience · 2026Review
- A brain-wide, trial- and time-dependent deterministic drive synergizes with within-trial noise to time self-initiated actions.bioRxiv : the preprint server for biology · 2026Article
- Multi-timescale Computation by Astrocytes.bioRxiv : the preprint server for biology · 2026Article
- DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping in different species.Cell reports methods · 2026Article
- Short- and long-term modulation of rat prefrontal cortical activity following single doses of psilocybin.Molecular psychiatry · 2025Article
- Interactions between motor cortical forelimb regions and their influence on muscles reorganize across behaviors.Nature communications · 2025Article
- Chemoarchitectural studies of the rat hypothalamus and zona incerta.bioRxiv : the preprint server for biology · 2025Article
- Linear and categorical coding units in the mouse gustatory cortex drive population dynamics and behavior in taste decision-making.bioRxiv : the preprint server for biology · 2025Article
- Induction of cortical ON/OFF periods in awake mice fulfills sleep functions.bioRxiv : the preprint server for biology · 2025Article
- A pipeline for mouse brain registration to an atlas after in vivo neurophysiological recordings.Anatomical science international · 2025Article
- A cellular basis for mapping behavioural structure.Nature · 2024Article
- A deep learning classification task for brain navigation in rodents using micro-Doppler ultrasound imaging.Heliyon · 2024Article
- The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases.Frontiers in neuroinformatics · 2024Article
- Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration.Nature methods · 2023Article
- Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment.bioRxiv : the preprint server for biology · 2023Article
- A neuroscientist's guide to using murine brain atlases for efficient analysis and transparent reporting.Frontiers in neuroinformatics · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recording technologies for rodents have seen huge advances in the last decade, allowing users to sample thousands of neurons simultaneously from multiple brain regions. This has prompted the need for digital tool kits to aid in curating anatomical data, however, existing tools either provide limited functionalities or require users to be proficient in coding to use them. To address this we created HERBS (Histological E-data Registration in rodent Brain Spaces), a comprehensive new tool for rodent users that offers a broad range of functionalities through a user-friendly graphical user interface. Prior to experiments, HERBS can be used to plan coordinates for implanting electrodes, targeting viral injections or tracers. After experiments, users can register recording electrode locations (e.g. Neuropixels and tetrodes), viral expression, or other anatomical features, and visualize the results in 2D or 3D. Additionally, HERBS can delineate labeling from multiple injections across tissue sections and obtain individual cell counts.Regional delineations in HERBS are based either on annotated 3D volumes from the Waxholm Space Atlas of the Sprague Dawley Rat Brain or the Allen Mouse Brain Atlas, though HERBS can work with compatible volume atlases from any species users wish to install. HERBS allows users to scroll through the digital brain atlases and provides custom-angle slice cuts through the volumes, and supports free-transformation of tissue sections to atlas slices. Furthermore, HERBS allows users to reconstruct a 3D brain mesh with tissue from individual animals. HERBS is a multi-platform open-source Python package that is available on PyPI and GitHub, and is compatible with Windows, macOS, and Linux operating systems.
Indexed as
Identifiers
What OpenQuestion holds
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.