Component

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.

Quote:

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.

This small plugin demonstrates the use of OpenSlide in java: it  will extract an imageJ roi drawn from the thumbnail of the whole slide image, or the full image at the desired resolution from an hammatsu NDPI file. Note that z stack are not supported by openslide (neitheir ndpiS).