ArticleeLife2022
Minian, an open-source miniscope analysis pipeline.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Article
- Miniscope Zero: a fully wireless, single-cell-resolution miniature microscope for imaging neural dynamics in freely behaving animals.bioRxiv : the preprint server for biology · 2026Article
- Striatal pathways dissociably control action counting and goal-directed steering.Nature neuroscience · 2026Article
- Dissociable roles of prefrontal plasticity in decision-making strategy and execution of habitual behavior.Nature communications · 2026Article
- Stars2Cells: Astrometric Tracking of Neurons Across Imaging Sessions.bioRxiv : the preprint server for biology · 2026Article
- Article
- State-dependent geometric transformations in the mouse hippocampus support fear generalization without loss of discriminability.bioRxiv : the preprint server for biology · 2026Article
- A Low-Parameter Adaptive Framework Based on Gaussian Mixture Modeling for Detecting Weak Astrocytic Calcium Signals in Two-Photon Imaging.Bioengineering (Basel, Switzerland) · 2026Article
- Hippocampal criticality tracks cognitive demand and shifts with memory impairment.Communications biology · 2026Article
- Basal ganglia output dynamically controls skilled forelimb kinematics in real time.bioRxiv : the preprint server for biology · 2026Article
- Dissecting neuronal circuit function and dysfunction in Alzheimer's disease mouse models: from conventional calcium imaging analysis to machine learning-based approaches.Frontiers in aging neuroscience · 2026Review
- The relevance of context in memory tasks influences the magnitude of hippocampal remapping.Cell reports · 2025Article
- Elucidating an anterior cingulate circuit for self-initiated actions and rescue of Parkinsonian akinesia.bioRxiv : the preprint server for biology · 2025Article
- Divergent prefrontal cortex circuits regulate cued food seeking under distinct metabolic or emotional states.Nature communications · 2025Article
- Striatal Pathways for Action Counting and Steering.bioRxiv : the preprint server for biology · 2025Article
- Article
- Decoding Secondary Motor Cortex Neuronal Activity During Cocaine Self-Administration: Insights From Longitudinal In Vivo Calcium Imaging.Biological psychiatry global open science · 2025Article
- Integrating optical neuroscience tools into touchscreen operant systems.Nature protocols · 2025Review
- Layer 1 NDNF interneurons form distinct subpopulations with opposite activation patterns during sleep in freely behaving mice.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- AI-Powered Mice Behavior Tracking and Its Application for Neuronal Manifold Analysis Based on Hippocampal Ensemble Activity in an Alzheimer's Disease Mice Model.International journal of molecular sciences · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Miniature microscopes have gained considerable traction for in vivo calcium imaging in freely behaving animals. However, extracting calcium signals from raw videos is a computationally complex problem and remains a bottleneck for many researchers utilizing single-photon in vivo calcium imaging. Despite the existence of many powerful analysis packages designed to detect and extract calcium dynamics, most have either key parameters that are hard-coded or insufficient step-by-step guidance and validations to help the users choose the best parameters. This makes it difficult to know whether the output is reliable and meets the assumptions necessary for proper analysis. Moreover, large memory demand is often a constraint for setting up these pipelines since it limits the choice of hardware to specialized computers. Given these difficulties, there is a need for a low memory demand, user-friendly tool offering interactive visualizations of how altering parameters at each step of the analysis affects data output. Our open-source analysis pipeline, Minian (miniscope analysis), facilitates the transparency and accessibility of single-photon calcium imaging analysis, permitting users with little computational experience to extract the location of cells and their corresponding calcium traces and deconvolved neural activities. Minian contains interactive visualization tools for every step of the analysis, as well as detailed documentation and tips on parameter exploration. Furthermore, Minian has relatively small memory demands and can be run on a laptop, making it available to labs that do not have access to specialized computational hardware. Minian has been validated to reliably and robustly extract calcium events across different brain regions and from different cell types. In practice, Minian provides an open-source calcium imaging analysis pipeline with user-friendly interactive visualizations to explore parameters and validate results.
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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.