Threshold and select objects imagej4/18/2024 ![]() Once the regional thresholds are computed, they are interpolated (bilinear interpolation) across the entire image yielding a threshold map. In our experience, regional threshold failures are rare. It is possible that thresholds fail all the way up the quadtree heirarchy, in which case a same threshold is applied to all regions which is identical to applying a global threshold. In such cases, the regional threshold is replaced by the threshold of its parent quadtree (if the parent's threshold doesn't fail). Occasionally, the regional threshold fails if the sum of the weights (the denominator) falls to the level of background containing only noise. In any case, if you choose to perform this type of adjustments, they should be clearly stated (preferably alongside their justification) in the method’s section.Error creating thumbnail: Unable to save thumbnail to destination If possible, you should perform any measurements in the original orientation. Bare in mind that by rotating an image by an arbitrary angle you’re inevitably losing some information due to interpolation. the object has a preferred/standard orientation that cannot be ensured during acquisition). Also, there should be a clear reason to rotate an image in the first place (e.g. I’d personally refrain from masking/coloring the background, specially around the object of interest, unless it’s clearly justified. the precise selection of the limits of the object has no bearing on the information you’re trying to present/extract), I would say it’s safe to do it. If you’re certain that the background is completely irrelevant (such as scanned objected, or a section mounted in a slide) AND the segmentation of the object itself would be trivial/non-consequential (i.e. Otherwise, its validity/acceptabilty would very much depend on the nature of the image and background you’re dealing with. If the journal has a specific policy regarding background adjustment, this method would obviously be unnacceptable. Would it be accptable for publishing in journals where they dont want any image background adjustment Run("Rotate.", "rotate angle=&feret_angle") Run("Rotate.", "angle=&feret_angle interpolation=Bilinear fill") Run("Restore Selection") //juggling again Run("Restore Selection") //juggling the original roi, in other contexts can be called from the ROI manager run("Translate.", "x=&dx y=&dy interpolation=None") //this is the "standard" way, but for RGB the next lines actually use the background color tMeasurements // alternative to measure-getResult, no table involvedĭx = round(getWidth()/2 - parseInt(List.get("X"))) ĭy = round(getHeight()/2 - parseInt(List.get("Y"))) įeret_angle = parseInt(List.get("FeretAngle")) You can use the one-line version, but will have to deal with the black border. Oh, I see! In order to avoid clipping, you should translate the object (and ROI) to the center of the image before rotating (as long as it fits within a circle of diameter = min(img_height, img_width)) Is there a way to remove a previously applied threshold? SO I can then use the same original threshold to re-sekect the rotated wing?Įxample images and the macro I am using can be found following the link provided (instead of re-posting it all again). the outline would move with the object when rotated and update in the ROI manager. Is there a way to rotate the ROI outline of the selected image with the image? - i.e. Perhaps because that threshold has already been applied. However, for some images the threshold method does not work well on the rotated image. However, in this macro (at step 3) I reselect the wing and make a new ROI using a threshold method. AS the ROI is divided into 3 sections using a vertical line - this may result in different areas being selected if the wing is at a different angle…īriefly this macro: 1) selects an object using a threshold 2) rotates the wing on its’ ferets angle 3) re-selectes the wing using another threshold (which is where the issue lies) 4) measures three sections of the re-selected and rotated object. The photos I am using are of butterfly wings. This is great but I has realised a potential issue. mean_grey_wing_thirds_multiFile.ijm (2.7 KB) It also works through all the sub-directories in a folder. I have made a macro script that takes an ROI and splits it into 3 parts and calculates the mean grey value per section. Divide ROI into 3 equal parts - align using ferets angle first Image Analysis ![]()
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