Bioimage informatics

This toolkit extracts Spherical Textures: Angular projections of 2D or 3D image objects with subsequent spherical harmonics analysis.

From the author summary: "We introduce a novel method to extract quantitative data from microscopy images by precisely measuring the distribution of intensities within objects in both 3D and 2D. This method is easily accessible through the object classification workflow of ilastik, provided the original image is segmented into separate objects. The method is specifically designed to analyze the convex region in objects, focusing on the variation in fluorescence intensity caused by differences in their shapes or patterns."

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.

3DeeCellTracker is a deep-learning based pipeline for tracking cells in 3D time-lapse images of deforming/moving organs.

The installation comprises a set of Jupyter notebooks and a library they depend on. The workflow steps include separate training and segmentation/tracking.

Examples of cell tracking from the reference publication are: ~100 cells in a freely moving nematode brain, ~100 cells in a beating zebrafish heart, and ~1000 cells in a 3D tumor spheroid.

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.