Stars
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
Converts a raw digitized polygon mesh to a clean mesh where all the occurrences of a specific set of "defects" are corrected. Holes, self-intersections, degenerate and non-manifold elements are all…
ShapeEmbedLite: a lightweight self-supervised representation learning model for 2D shape analysis
Fix common issues in Mach-O binaries for notarization
Scientific Dataset Quality Control and Data Exploration Tool
nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding boxes, and lasso. Trained on 120+ diverse 3D datasets, it sets a new stan…
7 sessions workshop about bioimage analysis
Napari plugin with tools for manual correction of tracking data.
QuPath extension to work with images through OMERO's APIs
A python algorithm for tracking cells in 3D deforming organs
aafkegros / BigTrace
Forked from UU-cellbiology/BigTraceFIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets
KeyCastr, an open-source keystroke visualizer
Theoretically Efficient and Practical Parallel DBSCAN
Cell population growth simulator implemented in Mastodon.
A napari reader and writer for the graph exchange file format (geff)
Reference implementation of the Graph Exchange File Format
Rxiv-Maker is a GitHub-native framework that converts markdown into a publication-ready PDF. It automates scientific preprint generation with a focus on reproducibility and version control
The official QuPath extension for InstanSeg
The ImageJ plugin to run deep-learning models
Conda Environment MAnager, a library to execute code in isolated environments.
Multimodal Cell tracking in VR with Deep Learning support
browsing large volumetric data and shapes
nnInteractive plugin for Napari - nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding boxes, and lasso. Trained on 120+ diver…