ArticleCell reports methods2024
SynBot is an open-source image analysis software for automated quantification of synapses.
Article in Cell reports methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- SynapTrack: An automated tool for synapse quantification.Journal of microscopy · 2026Article
- Long-term voluntary exercise reveals limited translation of hippocampal molecular responses into neuroprotection in 5xFAD mice.bioRxiv : the preprint server for biology · 2026Article
- Engineered nanosponges mitigate peripheral stress-induced neuroinflammation and restore cognitive function.bioRxiv : the preprint server for biology · 2026Article
- USP15 mutation associated with autism spectrum disorder alters progenitor fate and neuronal maturation in human brain organoids.Molecules and cells · 2026Article
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- Adolescent alcohol exposure disrupts astrocyte-synaptic structural and functional coupling in the male dorsal hippocampus.Molecular psychiatry · 2026Article
- ATP13A4 gates extracellular polyamine levels to control excitatory synaptogenesis.Nature communications · 2026Article
- Neuroligin-2 is ubiquitinated by Nedd4l to control developmental astrocyte morphogenesis.The Journal of cell biology · 2026Article
- SynAPSeg: A novel dataset and image analysis framework for deep learning-based synapse detection and quantification.PLoS computational biology · 2026Article
- Protocol to study synapse density or volume-SynDOVE-in brain using confocal microscopy and Imaris three-dimensional surface rendering software.STAR protocols · 2026Article
- Npas4 regulates synaptic development in the patch/striosome compartment and early affective vocalization in neonatal mice.Molecular brain · 2026Article
- Glutamatergic neuron-tumor synapses shape human glioblastoma cell states through radial glia plasticity.bioRxiv : the preprint server for biology · 2026Article
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- Article
- SynAPSeg: A novel dataset and image analysis framework for deep learning-based synapse detection and quantification.bioRxiv : the preprint server for biology · 2026Article
- Reprogramming of neuronal genome function and phenotype by astrocytes.bioRxiv : the preprint server for biology · 2026Article
- Post-Critical Period Transcriptional and Physiological Adaptations of Primary Sensory Cortex after Sensory Loss.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Transient synaptic refinement and glial adaptations after whisker denervation in adult mice.Frontiers in cellular neuroscience · 2026Article
- Neuroligin-2 is ubiquitinated by Nedd4l to control developmental astrocyte morphogenesis.bioRxiv : the preprint server for biology · 2025Article
- Microglial MyD88-dependent signaling influences extracellular matrix development and interneuron maturation in the hippocampus.bioRxiv : the preprint server for biology · 2025Article
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6 authors.
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Abstract
The formation of precise numbers of neuronal connections, known as synapses, is crucial for brain function. Therefore, synaptogenesis mechanisms have been one of the main focuses of neuroscience. Immunohistochemistry is a common tool for visualizing synapses. Thus, quantifying the numbers of synapses from light microscopy images enables screening the impacts of experimental manipulations on synapse development. Despite its utility, this approach is paired with low-throughput analysis methods that are challenging to learn, and the results are variable between experimenters, especially when analyzing noisy images of brain tissue. We developed an open-source ImageJ-based software, SynBot, to address these technical bottlenecks by automating the analysis. SynBot incorporates the advanced algorithms ilastik and SynQuant for accurate thresholding for synaptic puncta identification, and the code can easily be modified by users. The use of this software will allow for rapid and reproducible screening of synaptic phenotypes in healthy and diseased nervous systems.
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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.