janelia-cellmap / cellmap-segmentation-challengeLinks
Repository of scripts to facilitate participation in CellMap's segmentation challenge. This includes downloading data, simple setups for training 2D and 3D models, workflows for prediction and post-processing on out-of-memory arrays, and evaluation of results against validation data.
β39Updated last month
Alternatives and similar repositories for cellmap-segmentation-challenge
Users that are interested in cellmap-segmentation-challenge are comparing it to the libraries listed below
Sorting:
- πβ66Updated 2 weeks ago
- Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and other bioimage analysis problems based on pytorch.β109Updated last week
- Simple watershed and agglomeration library for affinity graphs.β25Updated last month
- β100Updated 3 weeks ago
- Utilities for building and using the CEM dataset for unsupervised pre-training and downstream tasks.β29Updated 2 years ago
- PyTorch implementation of 2D and 3D StarDist - Object Detection with Star-convex Shapesβ25Updated 2 years ago
- Open source volume electron microscopy (vEM) datasets for connectomics.β14Updated 11 months ago
- PyTorch Connectomics: segmentation toolbox for EM connectomicsβ179Updated this week
- Utils and convenience functions for large-scale bio-image analysis.β58Updated 2 months ago
- Official implementation of "A novel deep learning-based 3D cell segmentation framework for future image-based disease detection". (Howeveβ¦β22Updated 2 years ago
- Codebase for "A Foundation Model for Cell Segmentation"β110Updated 2 weeks ago
- π¬π₯ Automated Blood Vasculature Analysis of 3D Light-Sheet Image Volumesβ52Updated last year
- MorphoFeatures code and dataβ22Updated 2 years ago
- Experimental code and examples for: Automated analysis of whole brain vasculature using machine learningβ74Updated 4 years ago
- Transformer-based cell tracking for live-cell microscopyβ104Updated 2 weeks ago
- Robust 3D Neuron Tracing / General 3D tree structure extraction in Python for 3D images powered by the Rivulet2 algorithm. Pain-free Instβ¦β71Updated 2 years ago
- 3D Extension of the Cellpose Algorithm by Stringer et al., 2021.β35Updated 3 years ago
- Python package for deep learning based image to image transformationβ53Updated 2 months ago
- β21Updated 4 years ago
- Python scripts to read and write the CREMI hdf5 file format.β39Updated 2 years ago
- Convolutional Neural Network-Based Instance Segmentation Algorithm to Acquire Quantitative Criteria of Early Mouse Developmentβ32Updated 2 years ago
- β92Updated 4 months ago
- Easy Volumetric Segmentation with Deep Learningβ28Updated last week
- β240Updated last year
- Deep Learning for EM Connectomicsβ15Updated 3 years ago
- [WACV 2024] AnyStar: Domain randomized universal star-convex 3D instance segmentationβ16Updated last month
- panoptica -- instance-wise evaluation of 3D semantic and instance segmentation mapsβ26Updated last month
- Open source Python library for building bioimage analysis pipelinesβ184Updated last week
- β38Updated last year
- β188Updated last week