mjin1812 / SMARTLinks
Semi-manual alignment to reference templates (SMART): An open source pipeline in R for whole brain mapping
☆14Updated 4 years ago
Alternatives and similar repositories for SMART
Users that are interested in SMART are comparing it to the libraries listed below
Sorting:
- This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".☆16Updated 4 years ago
- COmmon COordinate FRAMEwork in R☆38Updated 5 years ago
- Example vignette for dotdotdot software☆18Updated 4 years ago
- R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single-cell RNA-seq data …☆16Updated 10 years ago
- Phenotypic variation of transcriptomic cell types in mouse motor cortex☆26Updated 4 years ago
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆35Updated 4 years ago
- R package for segmentation, registration and generating web-based brain atlases from microscope images☆93Updated 4 years ago
- Analysis of smFISH data☆12Updated 7 years ago
- EASI-FISH analysis pipeline for spatial transcriptomics☆35Updated last year
- Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.☆50Updated 4 years ago
- Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas☆98Updated this week
- Single cell RNA-seq analysis for transcriptomic type characterization☆38Updated 4 months ago
- Allen Brain Atlas utilities, parsers and data structures☆11Updated 8 years ago
- Tools and scripts for EASI-FISH image data analysis☆17Updated 3 years ago
- AllenDigger, a tool for spatial expression data visualization, spatial heterogeneity delineation and single cell registration based on Al…☆14Updated 2 years ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆39Updated 4 months ago
- Software for processing and analyzing STARmap experiments.☆38Updated 6 years ago
- Graph-based Decoding for In Situ Sequencing☆10Updated 5 years ago
- An automatic deep learning algorithm for spot detection in fluorescence microscopy images.☆26Updated last week
- Tool for precise, interactive, fast and scalable FISH spot detection☆50Updated last year
- ABBA, controlled from python☆18Updated 2 months ago
- Building Gene Sets and Mapping mFISH Data☆16Updated 5 months ago
- QC and cell type assignment for patch-seq transcriptomics data☆24Updated last year
- Algorithmic and Utility Extensions for the Imaris Program☆20Updated last week
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆35Updated last year
- Acquiring images from allen brain atlas, mouse ISH experiments in R.☆17Updated last year
- A self-explanatory, hands-on intro to bioimage analysis in python. Slightly outdated but still much liked by learners.☆99Updated 2 years ago
- Spatial analysis of FISH data☆34Updated 8 months ago
- A Python package using Gromov-Wasserstein distance to compare cell shapes☆22Updated 2 weeks ago
- Brain Cell Type Specific Gene Expression Analysis☆17Updated 2 years ago