Open source volume electron microscopy (vEM) datasets for connectomics.
☆19Oct 4, 2026Updated last month
Alternatives and similar repositories for awesome-vem-datasets
Users that are interested in awesome-vem-datasets 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 curated list of resources for 3D segmentation of neurites in EM images☆59Mar 11, 2024Updated 2 years ago
- Official implementation, datasets and trained models of "Masked Image Modeling for Generalizable Organelle Segmentation in Volume EM" (IE…☆11Mar 10, 2026Updated 7 months ago
- Official implementation, datasets and trained models of "SegNeuron: 3D Neuron Instance Segmentation in Any EM Volume with a Generalist Mo…☆24Sep 16, 2026Updated last month
- Collection of connectomic papers and datasets.☆16Dec 25, 2023Updated 2 years ago
- ☆10Feb 8, 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.
- Command line tool for registration of very large 3D volumes.☆16Jan 28, 2026Updated 9 months ago
- ☆12Mar 18, 2024Updated 2 years ago
- Utility functions for large-scale bio-image analysis.☆64Jul 1, 2026Updated 4 months ago
- 🌈☆70Oct 10, 2025Updated last year
- A framework for easy application of established machine learning techniques on large, multi-dimensional images.☆61Apr 24, 2026Updated 6 months ago
- Simple watershed and agglomeration library for affinity graphs.☆31Oct 6, 2026Updated last month
- A contrastive learning framework for 3D electron microscopy data☆13Jan 17, 2023Updated 3 years ago
- PyTorch Connectomics: segmentation toolbox for EM connectomics☆202Updated this week
- ☆11Aug 30, 2023Updated 3 years 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.
- ☆13Sep 28, 2025Updated last year
- NEURD: A mesh decomposition framework for automated proofreading and morphological analysis of neuronal EM reconstructions☆29Feb 24, 2026Updated 8 months ago
- Utilities for working with FIB-SEM data (Extract/analyze data, register FIB-SEM stacks, analyze noise etc.)☆14Sep 18, 2026Updated last month
- Comprehensive platform for automated large-scale connectomics. Segmentation and Detection models built upon Funke lab's algorithms.☆14Oct 28, 2026Updated last week
- Read and write Neuroglancer datasets programmatically.☆176Oct 27, 2026Updated last week
- A napari plugin for interactive Segment Anything Model 3 (SAM3) segmentation using text, points, boxes, exemplar prompts, point-based ref…☆19Sep 23, 2026Updated last month
- A tool for proofreading and refining synaptic polarity annotations in electron microscopy volumes.☆11Oct 7, 2026Updated 3 weeks ago
- Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari☆38Oct 30, 2026Updated last week
- This is an official implementation of the CVPR2022 paper "Blind2Unblind: Self-Supervised Image Denoising with Visible Blind Spots".☆145May 8, 2023Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Multilabel and Grey 3D morphological image processing functions. Dilate, Erode, Opening, Closing, Hole Filling.☆19Oct 30, 2026Updated last week
- Code to the paper "Self-Supervised Graph Representation Learning for Neuronal Morphologies"☆18Apr 5, 2024Updated 2 years ago
- A template repo used to make new napari plugins☆42Updated this week
- ImageJ/Fiji plugin for consistent elastic registration of 2D images☆27Oct 24, 2026Updated last week
- Automated Segmentation of cellular substructures in Electron Microscopy☆18Jan 28, 2026Updated 9 months ago
- Repository of scripts to facilitate participation in CellMap's segmentation challenge. This includes downloading data, simple setups for …☆43Jul 10, 2026Updated 3 months ago
- Tools for handling FIB-SEM data and annotations☆21Apr 4, 2025Updated last year
- ☆14May 10, 2024Updated 2 years ago
- Aligner for large scale serial section image data☆20Jul 7, 2023Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Deep Electron Microscopy Image Stitching (DEMIS): a tool for stitching grids of electron microscopy images. Image matching is performed u…☆19Dec 29, 2025Updated 10 months ago
- ☆68Oct 20, 2026Updated 2 weeks ago
- Finite-Element Assisted Brain Assembly System for stitching & alignment of connectomics data☆29Updated this week
- Visualize, share and annotate your large 3D images online☆187Updated this week
- Shared repo for EM connectomics and Array Tomography render based image processing modules☆18Updated this week
- ☆24Aug 26, 2026Updated 2 months ago
- AllenDigger, a tool for spatial expression data visualization, spatial heterogeneity delineation and single cell registration based on Al…☆14Apr 2, 2023Updated 3 years ago