Component

Trace ridges combines filtering, Watershed transforms, Edge detection and mathematical morphology to trace ridges in an image with fibre-like structures. 
Publication provides objective comparison of six existing methodologies (Edge detection, CT Fire, Scale Space, Twombli, U-Net and Graph Based).

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The Pairwise Stitching first queries for two input images that you intend to stitch. They can contain rectangular ROIs which limit the search to those areas, however, the full images will be stitched together. Once you selected the input images it will show the actual dialog for the Pairwise Stitching.

napari-lattice is a napari plugin designed for the analysis and visualization of Lattice Lightsheet Microscopy (LLSM) and Oblique Plane Microscopy (OPM) data, particularly focusing on data acquired from Zeiss Lattice Lightsheet systems. Also available as lls-core - a command line version of the same tool which does not require napari.

napari-lattice allows users to deskew and deconlolve lattice light sheet, or any oblique plane microscopy, data. To speed processing, users can provide ROIs to be cropped and processed separately.  This significantly speeds up processing time and allows many options for parallelisation. 

AnyLabeling is Effortless AI-assisted data labeling tool with AI support from Segment Anything and YOLO models!

AnyLabeling = LabelImg + Labelme + Improved UI + Auto-labeling

Installation

Standalone (executable)

The executable file links are provided in Assets section here

Install from source

git clone https://github.com/vietanhdev/anylabeling
cd anylabeling
pip install .

Install from PyPI

pip install anylabeling

With GPU support:

pip install anylabeling-gpu

PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.