#Imagej threshold to selection code

#Imagej threshold to selection code

I attach the code with one image if you want to see how it work (you can just run it, I left all the ROI produced so if you scroll them you will see what the macro does). In the case the AND produce a selection (because there is a plant in the subseted ROI) it will return a value different than -1. The selection type return the type of selection, in my case I use it after the AND, if there is no selection (because of an absence of plant) it does return -1

So I managed to “explain” to the macro how it have to deal whereas there is not a plant. Run('RGB Stack') run('Convert Stack to Images') Min=newArray(3) max=newArray(3) filter=newArray(3) a=getTitle() Ĭall('ij.') PS: I attach an image where the macro block. When the macro do the AND between the plant threshold and the position where there isn’t a plant, the result of the AND is null so when it try to add it still return “the active image does not have a selection”ĭo you think is possible to deal with dialogbox of the roimanager or with the result of the AND? LikeĪ) detect the opening of a dialog box with “the active image does not have a selection”ī) detect that the ROI resulting from the AND operation is 0 Unfortunatly it does not solve the problem. And here the for cycle that give me inconvenience Run('Create Selection') roiManager('Add') close() Hereafter I report the code: run('Color Threshold.') // thresholding I imagine that I can solve my problem using if/else and tell the macro to switch to the next images, but I have not idea which condition use. Some time, in some pots there isn’t a plant so while going through it’s work, the macro stop and say “the image does not have a selection”. Then it select always the ROI number 0 and ADD it to the rectangles made previously. Then it create different rectangle (one for each pot in the tray) and add it to the roiManager (ROI number 1,2,…x). The macro first threshold the images according the plants, make a selection and add it to the roiManager (ROI number 0). Having independent depth-cueing for surface (nearest-point) and interior (brightest-point) allows for more visualization possibilities.I am writing a macro to analyse in repetitive manner some plants in tray pots. For both kinds, depth-cueing is turned off when set to zero (i.e.100% of intensity in back to 100% of intensity in front) and is on when set at 0 < n 100 (i.e.( 100 − n)% of intensity in back to 100% intensity in front). Interior Depth-Cueing works only on brightest-point projections. Provides the ImageJ Auto Threshold plugin functionality to R users. Description Algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. Surface Depth-Cueing works only on nearest-point projections and the nearest-point component of other projections with opacity turned on. Type Package Title An R Port of the ImageJ Plugin Auto Threshold Version 1.4.2 Maintainer Rory Nolan. Two kinds of depth-cueing are available: Surface Depth-Cueing and Interior Depth-Cueing. The trade-off for this increased realism is that data points shown in a depth-cued image no longer possess accurate densitometric values. The depth-cueing parameters determine whether projected points originating near the viewer appear brighter, while points further away are dimmed linearly with distance. Surface/Interior Depth-Cueing Depth cues can contribute to the three-dimensional quality of projection images by giving perspective to projected structures.