DanuserLab / u-segment3DLinks
Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.
☆21Updated 2 months ago
Alternatives and similar repositories for u-segment3D
Users that are interested in u-segment3D are comparing it to the libraries listed below
Sorting:
- Guides and code for 3D nuclear instance segmentation☆22Updated 2 months ago
- SplineDist: Automated Cell Segmentation with Spline Curves☆67Updated 10 months ago
- Accurate and efficient spot detection for microscopy data☆95Updated 2 weeks ago
- A napari plugin for clustering objects according to their properties.☆87Updated last week
- StarDist plugin for ImageJ☆31Updated 3 years ago
- Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy☆74Updated 4 months ago
- Bringing the ZeroCostDL4Mic experience running everywhere via easy-to-install docker images☆80Updated this week
- ☆12Updated last year
- ☆87Updated 5 months ago
- Multiple file format reading directly into napari using pure Python☆37Updated last year
- Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)☆37Updated 3 months ago
- A module with convenience functions for writing Python code that interacts with OMERO.☆45Updated last week
- ZELDA: a 3D Image Segmentation and Parent to Child relation plugin for microscopy image analysis in napari☆20Updated 9 months ago
- Segmentation method able to detect membrane/nuclei-labelled cells with low signal-to-noise ratio and dense packing in 2D and 3D. Availabl…☆33Updated 2 weeks ago
- ☆16Updated last year
- A plugin based on scikit-image for segmenting nuclei and cells based on fluorescent microscopy images with high intensity in nuclei and/o…☆28Updated 3 months ago
- ☆51Updated 3 months ago
- ☆12Updated last month
- Transformer-based cell tracking for live-cell microscopy☆82Updated last week
- A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification☆23Updated 3 years ago
- Python-based Human-In-the-LOop Workflow: PHILOW is an interactive deep learning-based platform for 3D datasets☆26Updated 6 months ago
- LSTree is a digital organoid and lineage tree extraction workflow for light sheet movies.☆19Updated 2 years ago
- StarDist plugin for napari☆40Updated last year
- An automated point-set based registration algorithm for correlative light and electron microscopy (CLEM)☆18Updated 4 months ago
- MiC is an ImageJ plugin to compare segmentation masks☆19Updated 2 months ago
- ☆11Updated last year
- 3D Extension of the Cellpose Algorithm by Stringer et al., 2021.☆35Updated 2 years ago
- Napari Visualization tool for Trackmate > 6.0 XML files for 2/3D + time tracks. Available via pip package napatrackmater.☆17Updated 2 weeks ago
- QuPath extension for Cellsparse☆19Updated 3 months ago
- ☆19Updated 3 weeks ago