The result is a “semantic mask”, where object/tissues of the same group have the same pixel value. There ROIs are turned to a region with pixel values value corresponding to the ROI group.

This plugin takes advantage of the group attribute of ROIs to annotate regions belonging to the same “object-class”, tissue… Overlapping ROIs will thus be merged into a single “white blob” in the mask. The resulting mask is black (pixel value 0) while regions outlined by rois are turned to white pixels (pixel value 255). There are 2 plugins for the generation of: One mask will be generated for every image in the stack. In the latter case, the Z-Position of the Rois is used to associate them to the corresponding image. Single images or multiple images in a stack (or Virtual stack) can be annotated.

The plugin should be executed after having annotated all ROIs in an image (stored in the RoiManager), or all image-slices of a stack. It can be used for instance to generate ground-truth segmentation masks.Īnnotated images can be single plane images or stacks with a single dimensions slider, HYPERSTACKS ARE CURRENTLY NOT SUPPORTED. These plugins facilitate the generation of masks from image-regions outlined with ROIs for large datasets. The plugins are then available at the bottom of the menu Edit > Selection, the Mask from Rois entry. This will automatically copy the files in the right location. Unzip the file, drag and drop the Fiji.app directory in the directory containing your Fiji installation (ie in the directory containing your own Fiji.app). Generate Masks from Rois in Fiji InstallationĪctivate the Masks from Rois update site (see Activating an update site).Īlternatively, without the Fiji updater, you can download the content of the repository, clicking the green button code, and choosing Download ZIP.

MASKA download the new version for mac