Component

Viv is a JavaScript library providing utilities for rendering primary imaging data. Viv supports WebGL-based multi-channel rendering of both pyramidal and non-pyramidal images. The rendering components of Viv are provided as Deck.gl layers, facilitating image composition with existing layers and updating rendering properties within a reactive paradigm.

TrackMate based tracker to be used when uploading integer labelled segmentation images, coming from a Deep Learning tool such as stardist. To use this tool efficiently we provide a python notebook to collect/localize the position of cells, this step creates a CSV file which can then be loaded into the Fiji tracker to do particle tracking with TrackMate interface.

MSER based on implementation in imglib2 provided as an interactive GUI tool for spot detection in 2/3/4D images.

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LaRoME = Label + Region Of Interest + Measure

Label image (aka Count Masks): An image in which pixels of an object have all the same value. Each object has a unique value.

Measurement image: An image in which pixels of an object have all the same value, corresponding to a measurement (Area, Angle, Mean...)

Using a Hamamatsu slide scanner such as the NanoZoomer, you may end up with NDPI files that can't always be directly open in standard image analysis software such as ImageJ. NDPITools is a collection of software that can convert NDPI files to standard TIFF files, possibly cutting them into smaller JPEG or TIFF pieces that will better fit into your computer's memory. It comes with a bundle of plugins for ImageJ which enable the use of the software directly inside ImageJ with point-and-click.