mjin1812 / SMART
Semi-manual alignment to reference templates (SMART): An open source pipeline in R for whole brain mapping
☆14Updated 3 years ago
Related projects ⓘ
Alternatives and complementary repositories for SMART
- This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".☆15Updated 3 years ago
- R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single-cell RNA-seq data …☆17Updated 9 years ago
- COmmon COordinate FRAMEwork in R☆36Updated 4 years ago
- Single cell RNA-seq analysis for transcriptomic type characterization☆30Updated this week
- Example vignette for dotdotdot software☆18Updated 3 years ago
- Acquiring images from allen brain atlas, mouse ISH experiments in R.☆15Updated 8 months ago
- Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas☆51Updated this week
- Phenotypic variation of transcriptomic cell types in mouse motor cortex☆24Updated 3 years ago
- AllenDigger, a tool for spatial expression data visualization, spatial heterogeneity delineation and single cell registration based on Al…☆13Updated last year
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆35Updated 3 years ago
- Human cortical cell types☆24Updated 5 years ago
- Repository for storing prototype functionality implementations for the BKP☆18Updated this week
- R package for segmentation, registration and generating web-based brain atlases from microscope images☆86Updated 3 years ago
- Building Gene Sets and Mapping mFISH Data☆16Updated last year
- EASI-FISH analysis pipeline for spatial transcriptomics☆33Updated this week
- Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.☆47Updated 3 years ago
- Allen Brain Atlas utilities, parsers and data structures☆10Updated 7 years ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆24Updated 2 months ago
- An automatic deep learning algorithm for spot detection in fluorescence microscopy images.☆16Updated 3 weeks ago
- Brain Cell Type Specific Gene Expression Analysis☆14Updated 10 months ago
- Code for preparing and running the imageCCA method.☆20Updated 7 years ago
- This repository contains code to generate standardized cell type nomenclature from an R "dendrogram".☆13Updated 2 years ago
- Software for processing and analyzing STARmap experiments.☆34Updated 5 years ago
- Code for the image processing and analysis described our Nature Protocols paper.☆10Updated 9 years ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆35Updated last year
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆41Updated 4 months ago
- Code accompanying the manuscript "Broad transcriptomic dysregulation across the cerebral cortex in ASD".☆13Updated 2 years ago
- ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.☆51Updated 4 years ago
- Toolbox for the analysis of smFISH images.☆57Updated last year
- VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps☆41Updated 8 months ago