fmi-basel / LSTree
LSTree is a digital organoid and lineage tree extraction workflow for light sheet movies.
☆18Updated last year
Alternatives and similar repositories for LSTree:
Users that are interested in LSTree are comparing it to the libraries listed below
- Particle tracking by solving linear assignment problem.☆50Updated last week
- "Defragmentation: bringing BioImage Analysts to the cloud!” training school for the new generation of bioimage analysts. Topics: workflow…☆15Updated last year
- FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets☆29Updated 2 months ago
- A plugin based on scikit-image for segmenting nuclei and cells based on fluorescent microscopy images with high intensity in nuclei and/o…☆26Updated 5 months ago
- Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 2/3D + time tracks. Available via pip package napatrackmater.☆16Updated last week
- some useful function to get Label from ROIs and vice versa , and more!☆12Updated last year
- Python-based Human-In-the-LOop Workflow: PHILOW is an interactive deep learning-based platform for 3D datasets☆26Updated 2 months ago
- ☆49Updated 6 months ago
- dask empowered fast4dreg☆11Updated 4 months ago
- Browse your OMERO database from within napari.☆36Updated 2 weeks ago
- A module with convenience functions for writing Python code that interacts with OMERO.☆44Updated last week
- ZELDA: a 3D Image Segmentation and Parent to Child relation plugin for microscopy image analysis in napari☆20Updated 4 months ago
- A napari plugin for clustering objects according to their properties.☆83Updated this week
- StarDist plugin for napari☆38Updated 7 months ago
- ☆23Updated this week
- Automated mitochondrial segmentation and tracking.☆31Updated 3 years ago
- Multi-Object Tracker using Integer Linear Equations☆30Updated 3 weeks ago
- Track and lineage visualization with btrack and Napari☆45Updated 5 months ago
- ☆69Updated 2 months ago
- ☆12Updated 11 months ago
- Fast4DReg is a Fiji script for quick drift correction in time-lapse 3D-stacks. The script can be used to correct drift in all x-, y- and/…☆39Updated 4 months ago
- napari plugin for trackastra☆13Updated 6 months ago
- Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)☆36Updated last month
- This repository hosts notebooks, information and data for the Quantitative Bio-Image Analysis with Python Course 2022.☆15Updated 2 years ago
- A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification☆23Updated 3 years ago
- Interactive visualization and sharing of cell tracking data in the browser☆23Updated 3 weeks ago
- Feature extraction for labeled objects in images using regionprops from scikit-image☆50Updated 6 months ago
- Tools for distributed alignment of massive images☆81Updated last week
- A short course exploring several fun and useful notebooks and Napari widgets for deep learning with SAM, Cellpose, Stardist and friends.☆14Updated last week
- Accurate and efficient spot detection for microscopy data☆74Updated this week