MERlin is an extensible analysis pipeline applied to decoding MERFISH data
☆37Sep 21, 2021Updated 4 years ago
Alternatives and similar repositories for MERlin
Users that are interested in MERlin are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Bayesian Segmentation of Spatial Transcriptomics Data☆212Jul 31, 2026Updated last month
- ☆15Feb 28, 2022Updated 4 years ago
- MERFISHTools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data. On top, they provi…☆14Aug 9, 2019Updated 7 years ago
- A writer and reader for NGFF OME-Zarr datasets☆14Nov 2, 2021Updated 4 years ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆41Apr 30, 2026Updated 4 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Test genes for Spatial Variation☆15Dec 20, 2024Updated last year
- DeepSpot is a deep learning method for the enhancement of mRNA fluorescent spots in microscopy images☆15Dec 1, 2021Updated 4 years ago
- Tool for precise, interactive, fast and scalable FISH spot detection☆54Feb 4, 2025Updated last year
- SpatialCorr: Identify gene sets with spatially varying correlation☆18Jan 2, 2024Updated 2 years ago
- Neuroscience/electrophsyiology data analysis tools (mostly Matlab)☆14May 28, 2019Updated 7 years ago
- Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.☆51Aug 1, 2021Updated 5 years ago
- Deep Learning Library for Spot Detection☆24Jun 4, 2026Updated 2 months ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆89Nov 16, 2025Updated 9 months ago
- starfish: unified pipelines for image-based transcriptomics☆250Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Toolkit for single-cell analysis of chromatin accessibility☆13Feb 27, 2020Updated 6 years ago
- Python package for conversions between ENSEMBL IDs and gene names (annotables + pyensembl)☆11Feb 2, 2026Updated 7 months ago
- ☆13Mar 29, 2024Updated 2 years ago
- Code for the paper on t-SNE with variable degree of freedom☆25Aug 5, 2020Updated 6 years ago
- MERFISH decoding software☆29Aug 16, 2025Updated last year
- ☆22Jul 3, 2019Updated 7 years ago
- An open and interoperable data framework for spatial omics data☆388Updated this week
- Workflows and analysis of scRNA-seq of Olfactory Projection Neurons for Li, Horns et al. (2017)☆21Aug 17, 2017Updated 9 years ago
- Interpretable model of sub-cellular RNA localization.☆12Dec 19, 2022Updated 3 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆106Dec 11, 2023Updated 2 years ago
- ☆27Jun 16, 2023Updated 3 years ago
- ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration☆181Aug 7, 2026Updated 3 weeks ago
- Trend Filter Denoising☆22Jul 30, 2021Updated 5 years ago
- A performant scientific image visualization system.☆36Aug 5, 2026Updated 3 weeks ago
- ☆27Apr 15, 2025Updated last year
- Source code of SACD(Super-resolution with Auto-Correlation two-step Deconvolution)☆13Dec 12, 2022Updated 3 years ago
- Small Routines for Plasma Physics Education☆10Updated this week
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆48Jul 16, 2024Updated 2 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- ☆31Apr 26, 2024Updated 2 years ago
- A Python toolbox for Fast Image Signal Separation Analysis, designed for Calcium Imaging data.☆34Updated this week
- Automated batch processing of cell and tissue microscopy image data in Napari☆22Updated this week
- Hera-T, a fast and accurate tool for estimating gene abundances in single cell data generated by the 10X-Chromium protocol☆18Nov 9, 2021Updated 4 years ago
- ☆16Apr 29, 2024Updated 2 years ago
- A repository of neural manifold techniques described and compared in "Neural manifold analysis of brain circuit dynamics in health and di…☆35Oct 6, 2023Updated 2 years ago
- EASI-FISH analysis pipeline for spatial transcriptomics☆36Apr 15, 2026Updated 4 months ago