manually align specimens to annotated 3D spaces
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May 10, 2023 - Python
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allen-brain-atlas
Here are 20 public repositories matching this topic...
🐭 Acquiring images from allen brain atlas, mouse ISH experiments in R.
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Mar 20, 2024 - R
Load and plot Allen connectivity data in MATLAB/Python
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May 26, 2026 - Jupyter Notebook
Python package for easy interaction with the Allen Institute for Brain Science
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Apr 20, 2017 - Python
Open-source image alignment and brain atlas registration for Fiji / ImageJ2. Review mouse brain microscopy against Allen CCFv3, select anatomical ROIs, and export crops and masks. Supports resumable batch review.
java open-source imagej imagej2 fiji neuroscience roi microscopy image-registration allen-brain-atlas histology image-alignment brain-atlas bioimage-analysis immunofluorescence roi-analysis atlas-registration ccfv3
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Sep 11, 2026 - Java
Generate a package-manager-friendly archive of ABI connectivity maps registered in SAMRI standard space.
linux gentoo fmri portage allen-brain-atlas package-management histology cell-biology fmri-data-analysis mouse-brain-mri
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Oct 30, 2024 - Python
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Sep 26, 2021 - Jinja
obsBrain: Observatory of Brain
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Apr 29, 2021 - R
Generate a package-manager-friendly archive of ABI gene expression maps registered in SAMRI standard space.
linux gentoo fmri portage allen-brain-atlas molecular-biology package-management histology fmri-data-analysis mouse-brain-mri
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Oct 30, 2024 - Python
Ontologized versions of the ABA structureGraphs - with mappings to Uberon
ontology neuroinformatics allen-brain-atlas anatomy uberon neuroanatomy brain-data anatomy-ontology aba-uberon
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May 30, 2023 - Python
Reproducible analysis code for morphology–physiology coupling in mouse and human cortical neurons from the Allen Cell Types Database.
python reproducible-research neuroscience computational-neuroscience electrophysiology neuroinformatics allen-brain-atlas sholl-analysis neuronal-morphology
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Oct 4, 2026 - Python
Image Slicing with overlap. Takes an image, asks for user input about the number of rows and columns and slices into even parts. Customizable parameters.
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Mar 11, 2023 - Python
Building an ontology of specialised neuron types from data - well supported terms may later migrate to CL.
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Feb 7, 2019 - Jupyter Notebook
Neural decoding of visual stimulus properties from 2-photon calcium imaging data in mouse V1.
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Apr 17, 2026 - MATLAB
Interactive mapping of dissected tissue pieces to the Allen mouse brain atlas
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Sep 4, 2026 - Python
AxonLM: Neuroanatomical connectivity is linearly decodable from transformer FFN activations. AUC=0.963 on Allen Brain Atlas.
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May 4, 2026 - Python
End-to-end spatial transcriptomics pipeline for 10x Genomics Visium human brain glioblastoma — cell type annotation, GBM subtype characterization, and spatial neighborhood analysis
python nextflow computational-biology neuroscience bioinformatics-pipeline allen-brain-atlas umap 10x-genomics glioblastoma spatial-transcriptomics tumor-microenvironment scanpy cell-type-annotation visium squidpy singlecell-data-analysis leiden-clustering moran-statistics
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May 7, 2026 - Jupyter Notebook
Machine learning analysis of AlleHuman Brain Atlas gene-expression data to classify broad human brain regions across donors.
python machine-learning bioinformatics scikit-learn neuroscience gene-expression transcriptomics allen-brain-atlas
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Sep 15, 2026 - Jupyter Notebook
Personal site of Evyatar Swissa, neuroscientist — built with Vite and three.js around a point-sampled Allen mouse brain
portfolio webgl threejs personal-website neuroscience data-visualization allen-brain-atlas optogenetics vite
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Oct 10, 2026 - JavaScript
Integrative analysis tool combining Allen Brain Atlas connectivity and gene expression data for pain circuit profiling
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Mar 27, 2026 - Python
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