multi-channel

A Python toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.

FishFeats: napari plugin to perform quantification of multimodal labeling at the single-cell level in 3D tissues.

FishFeats allows to perform together in the same pipeline several analysis to quantify epithelia cells in 3D tissue, analysing cell morphology, nuclei, immuno-staining or RNA expression. The plugin allows flexibility to let the user choose the relevant step for a specific biological question.

This plugin is able to stitch an arbitrary collection or grid of images, it does not matter if it is 2d, 3d, 4d or 5d images as long as all images are of the same type. In contrast to the Pairwise Stitching of two images, this plugins will load (and potentially save) the images from/to harddisc.

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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.