mjin1812 / SMART
Semi-manual alignment to reference templates (SMART): An open source pipeline in R for whole brain mapping
☆14Updated 3 years ago
Alternatives and similar repositories for SMART:
Users that are interested in SMART are comparing it to the libraries listed below
- This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".☆15Updated 4 years ago
- COmmon COordinate FRAMEwork in R☆36Updated 4 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
- Example vignette for dotdotdot software☆18Updated 3 years ago
- Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas☆60Updated this week
- Phenotypic variation of transcriptomic cell types in mouse motor cortex☆25Updated 3 years ago
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆35Updated 3 years ago
- EASI-FISH analysis pipeline for spatial transcriptomics☆33Updated 4 months ago
- R package for segmentation, registration and generating web-based brain atlases from microscope images☆88Updated 3 years ago
- Single cell RNA-seq analysis for transcriptomic type characterization☆36Updated last week
- Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.☆50Updated 3 years ago
- An automatic deep learning algorithm for spot detection in fluorescence microscopy images.☆18Updated 2 months ago
- Graph-based Decoding for In Situ Sequencing☆10Updated 4 years ago
- Repository for storing prototype functionality implementations for the BKP☆24Updated last week
- AllenDigger, a tool for spatial expression data visualization, spatial heterogeneity delineation and single cell registration based on Al…☆14Updated last year
- Toolbox for the analysis of smFISH images.☆59Updated last year
- Building Gene Sets and Mapping mFISH Data☆16Updated last year
- Files associated with the From Samples To Knowledge 2025 QuPath training course☆11Updated 3 weeks ago
- Tool for precise, interactive, fast and scalable FISH spot detection☆48Updated last month
- Allen Brain Atlas utilities, parsers and data structures☆11Updated 7 years ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆36Updated last year
- The official QuPath extension for InstanSeg☆14Updated this week
- Tools and scripts for EASI-FISH image data analysis☆17Updated 2 years ago
- AICS Segmentation (One-Way) Mirror☆45Updated 4 years ago
- Code for the image processing and analysis described our Nature Protocols paper.☆10Updated 9 years ago
- QuPath extension to interactively align images☆22Updated 3 months ago
- Analysis of smFISH data☆11Updated 6 years ago
- Acquiring images from allen brain atlas, mouse ISH experiments in R.☆15Updated last year
- Spatial analysis of FISH data☆29Updated 9 months ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆27Updated 6 months ago