Fiji imagej contour3/14/2024 ![]() This detector is not part of the core Fiji distribution. It is documented here: trackmate-label-image-detector TrackMate-Ilastik This detector is also part of the core of TrackMate. This allows resolving them even if they touch each other. Object #2 will have the pixel value 2, etc. For instance, the object #1 in a label image will be made from all the pixels that have a pixel value of 1, over a black background of 0. In a label image, each object is represented by different integer values. If a segmentation algorithm can detect them, but outputs a black and white mask, they will appear as one object in the mask if they share a border. Indeed, in some cases you might have different objects that are so close that they touch each other. Label images are especially convenient as an output of segmentation algorithms. It is documented here: trackmate-thresholding-detector Label image detector You have to specify a threshold value to segment the objects. ![]() The thresholding detector creates objects from a grayscale image (it can be one channel in a multi-channel image). It is documented here: trackmate-mask-detector Thresholding detector ![]() This detector is part of the core of TrackMate. The objects will be built based on all the pixels have a value strictly larger than 0, which solves the issue of having a mask on 8-bit, 16-bit or 32-bit images. You can add the mask as an extra channel in the source image. This detector creates objects from a black and white channel in the source image. Detectors with segmentation capabilities Mask detector This page lists the eight detectors that have been introduced by this version, and links to their documentation and installation procedure. So we integrated the ilastik, MorphoLibJ, StarDist, cellpose and Weka plugins as detectors in TrackMate. But we also looked to integrate the state-of-the-art segmentation algorithms shipped with Fiji that do so. We used this new API to build simple detectors that can produce objects from a label image, a mask or a grayscale image with a threshold. Starting with version 7.0.0, TrackMate offers the possibility to segment objects, and store, display and quantify their shape.
0 Comments
Leave a Reply.AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |