#Imagej threshold selection dialog code#

Run the command “Create Selection” and add the resulting ROI to the RoiManager. Starting point: you have one or more ROIs created in the RoiManager. Maybe it’s a little late for a quick answer, but it could help someone else with the same issue. Msg = 'An image of the analysis is automatically saved, change filter settings if needed' ImageCalculator('AND create', 'Result of 0','2') Autogenerated macro, single images only! Msg = 'Use selection tools and backspace to remove all non plaque tissue' Msg = 'Trace the outline of the vessel and press OK.' Run('Set Measurements.', 'area area_fraction display scientific redirect=None decimal=3') Run('Set Scale.', 'distance=0 known=0 pixel=1 unit=pixel') Msg = 'Open image file, image area is calculated in pixels to calculate area size multiply with pixel size.'

You can also modify the macro below to your needs. Then close your image window and reopen, select the ROIs you want to display and flatten. So make your ROIs and clear everything outside, then select all (this is important so your’re ROIs are eventually ending up at the same spot in your picture) and do your thresholding and make a ROI from that and fill with some color. So this is then my before analysis and after analysis picture.įor you, you probably don’t need all of the selection steps. The ROIs are still present in the ROI editor, then the macro displays all on the image, then the image is flattened and safed in the same folder as ' original image name analyzed.tif'. So the macro closes the image and reopens it so the original image is there. So then I have all the ROIs I need but my original picture is green except for the plaque area. Then I want to know the collagen content (blue) of the plaque and select that with another color filter, and make it a ROI (ROI 2), and measure it. (magenta, a bit sloppy but you get the idea) Then I only want the plaque, so I select everything with the freehand tool outside the plaque area but inside the red line and delete with backspace, and select the plaque area based on the green background color filter and make it a ROI (ROI 1) and measure it. For me that is first the vessel area that I want to measure and make it a ROI (ROI 0) and give it a red line (everything outside of it I don’t need, so in the macro the outside of this ROI is cleared). So what the macro does is:įirst you can select the area you are interested in. I can imagine you don’t need it anymore since your post was some time ago, but for other people that need to do similar analysis it might be useful. I could not find it, so I made a macro for it. % Set background pixels where BW is false to zero.I was kind of looking for a similar macro to measure and save the analysis of collagen content of atherosclerotic lesions. % Initialize output masked image based on input image.

% Create mask based on chosen histogram thresholds % Define thresholds for channel 3 based on histogram settings % Define thresholds for channel 2 based on histogram settings % Define thresholds for channel 1 based on histogram settings % Auto-generated by colorThresholder app on 0 %- % Convert RGB image to chosen color space The % segmentation mask is returned in BW, and a composite of the mask and % original RGB images is returned in maskedRGBImage. The colorspace and % range for each channel of the colorspace were set within the app.

#Imagej threshold selection dialog code#

% = createMask(RGB) thresholds image RGB using % auto-generated code from the colorThresholder app. %createMask Threshold RGB image using auto-generated code from colorThresholder app. For this example, the background color is lighter near the bottom of the image.įunction = createMask(RGB) This automatic thresholding does not create a clean segmentation of the background and foreground, especially at the lower border between the foreground and background. The Y, Cb, and Cr color controls change to reflect the segmentation. If you want to delete a region you drew and start over, right-click anywhere in the region and select Delete Freehand.Īfter drawing the region, Color Thresholder automatically thresholds the image based on the colors you selected in the region you drew. Click the lasso icon in the axes toolbar at the top-right corner of the image and draw an ROI on the background. You can invert the mask later using the Invert Mask option.ĭefine a region using the freehand ROI tool. Because the background (purple cloth) is close to a uniform color, segment it rather than the foreground objects (the peppers). First, segment the image using automatic thresholding.