Reconstructing True 3D Spatial Omics at Single-Cell Resolution
☆24May 13, 2026Updated 5 months ago
Alternatives and similar repositories for DeepSpatial
Users that are interested in DeepSpatial are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A generative model to predict gene expression dynamics, cell population changes, and perturbation outcomes from time-series single-cell d…☆15Apr 17, 2025Updated last year
- A lightweight, ultrafast and general embedding framework for large-scale spatial omics data☆37Oct 16, 2026Updated last week
- Python library for brain-wide quantification and spatial analysis.☆12Jun 26, 2026Updated 4 months ago
- ABBA, controlled from python☆21Oct 15, 2026Updated 2 weeks ago
- [NeurIPS 2025] Implementation for the paper "Modeling Microenvironment Trajectories on Spatial Transcriptomics with NicheFlow"☆30Nov 4, 2025Updated 11 months ago
- 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.
- Image pyramid reader and writer enhanced with bio-formats library reader☆13Aug 30, 2023Updated 3 years ago
- UNRAVEL: UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images☆14Oct 22, 2026Updated last week
- Library to extract embeddings for DNA sequences using BioFM genomics foundation model☆22Aug 13, 2025Updated last year
- Tiled processing of arbitrarily large images — any image, any function.☆18Oct 22, 2026Updated last week
- [ICML 2025] Code for SUICA: Learning Super-high Dimensional Sparse Implicit Neural Representations for Spatial Transcriptomics.☆21Nov 22, 2025Updated 11 months ago
- A tool for translating between common coordinate frameworks using deformation matrices.☆17Oct 15, 2026Updated 2 weeks ago
- Anatomical space conventions made easy.☆13Oct 13, 2026Updated 2 weeks ago
- How to use Aligning Big Brains and Atlases with Python☆14May 3, 2023Updated 3 years ago
- Snakemake workflow for somatic mutation detection without matched normal samples☆14Mar 4, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data☆13Sep 29, 2024Updated 2 years ago
- ☆14Nov 12, 2025Updated 11 months ago
- Image registration and ROI matching for microscopy images using nuclei constellations☆17Updated this week
- Enhanced stain normalization for histopathology images with batch processing support. Optimized for CPU, GPU (CUDA), and MPS (Apple Silic…☆26Aug 9, 2026Updated 2 months ago
- ☆40Jun 11, 2026Updated 4 months ago
- A command-line tool to capture hierarchical relationships at scale☆20Updated this week
- ☆22Sep 20, 2026Updated last month
- Integrative and Reference-Informed Spatial Domain Detection for Spatial Transcriptomics☆47Feb 19, 2026Updated 8 months ago
- Teaching materials and outline for the Pasteur Bioimage Analysis vour☆17Jun 2, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- scNODE: Generative Model for Temporal Single Cell Transcriptomic Data Prediction☆36Oct 11, 2024Updated 2 years ago
- Learning stochastic dynamics from snapshots through regularized unbalanced optimal transport (ICLR'25 oral)☆37Dec 10, 2025Updated 10 months ago
- ☆13Mar 16, 2026Updated 7 months ago
- Conversion of neuroimaging data for display in Neuroglancer☆31Aug 19, 2026Updated 2 months ago
- [ICML 2024] VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling☆10Sep 22, 2024Updated 2 years ago
- Original materials for the "Introduction to Solving Biological Problems with Python" 2 days course☆10Jun 25, 2018Updated 8 years ago
- ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing☆23Jul 4, 2022Updated 4 years ago
- ☆16Oct 29, 2025Updated last year
- An R package for performing cell typing in SMI and other single cell data☆56May 1, 2026Updated 5 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Extract surfaces from 3D microscopy images and project them to 2D for analysis and visualization☆12Jul 17, 2026Updated 3 months ago
- Automated batch processing of tissue microscopy image data with a text-based interface☆10Mar 24, 2026Updated 7 months ago
- Projection operator method for statistical data analysis☆10Mar 11, 2025Updated last year
- Initial public release of code, data, and model weights for ADAF.☆12Feb 27, 2026Updated 8 months ago
- Neuroscience Landscape☆37Jul 26, 2024Updated 2 years ago
- INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation dataset…☆11Dec 12, 2022Updated 3 years ago
- A mouse brain histology tool for neuroscientists.☆13Feb 16, 2026Updated 8 months ago