![]() ![]() ![]() The main problem with measuring density by tile is that the boundaries are rather arbitrary. What is the best way to quantify this? Percentage area difference between the total annotation and the thresholded area? How would I segment these areas to each region of interest? When I’ve created an annotation from the density map GUI it puts it over the entire image, it would require the annotation to be split per each annotation region. This isn’t a huge priority, but it would be good to look at different density levels. How can we create multiple thresholds? I haven’t seen an option to add the density mapping value to objects. I am pretty happy with this method but im absolutely open to trying to get the density mapping to work. Where 2500 is the square area of my tiles in microns, so for instance using 50um tiles: 50 * 50 = 2500 Expand annotations by a fixed distance, and merge with others of the same class Define annotations as the newly created objects third is to select newly created annotationsĬreateAnnotationsFromPixelClassifier(classifier_name, initial_filter_size, initial_fill_size, "SELECT_NEW") First argument is minimum area, second is area to fill, Create annotations from a vessel pixel classifier. Specify which annotations to perform vessel segmentation in. SelectObjectsB圜lassification(vessel_name) Resolution=getCurrentImageData().getServer().getPixelCalibration().pixelHeightMicrons Training data must be properly categorized and annotated for a specific use case. Neighbour_merge_distance/=2 //Divide value by 2 because both adjacent objects will be dilated by this value (e.g. Data annotation is the categorization and labeling of data for AI applications. Must have 2 classes, vessels defined in `vessel_name` and Ignore*ĭef vessel_name="CD31+ vessel" //name of vessel objects generated from classifier number of microglia per mm^2, percent area occupied by microglia), you can use the following script: import static .QPEx.*ĭef initial_filter_size=20.0 //Do not create objects from classifier with a size smaller than thisĭef initial_fill_size=10000.0 //Fill objects in classifier with a size less than this (similar to fill holes)ĭef neighbour_merge_distance=10.0 //Merge vessel objects into one object if they exist within a certain distanceĭef shrink_objects=2.0 //Shrink objects by this valueĭef final_filter_size=20.0 //Delete any objects with an area less than thisĭef classifier_name="aSMA-GFAP-CD31 vessels" //name of classifier to make annotations from, verified using a trained classifier. tile detections converted to annotations), and you want to append some custom measurement to the parent annotation relating to your detections (e.g. ![]()
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