Thanks so much everyone for suggesting so many ways. Thanks, Herbie, yes, that's the last option I thought. :-)
I really like Ankit's proposal as it's very much automated. The idea given by Michael -- I am kind of doing that for finding the spacing between the consecutive petal like patterns. But, that doesn't give me a good estimate for all of my images, as it is just one type of pattern. I also like Curtis's idea, I need to play with that as suggested for the various patterns to see which one works the best. I really appreciate your valuable time and suggestions. Thanks, Anu On Saturday, March 9, 2024, Curtis Rueden <[email protected]> wrote: > Hi Anu, > > I think your segmentation can be automated, but it is a bit tricky. Here is > a quick attempt I made: > > 1. Labkit - https://imagej.net/plugins/labkit/ > This is a machine-learning based pixel classification, where you do manual > painting over the different areas of your image. Then train it, and paint > again over the parts it got wrong. Repeat until it learns well how things > should be. > > Here is how it looked for me after I did this process back and forth a > couple of times: > > [image: labkit-small.png] > > As you can see, it is not perfect, but it gets close enough that you can > then do additional steps afterward to extract the information you want. > Then, you can save the classifier and apply it to as many other similar > images as you want. > > Note that Labkit (at least in my hands today) has an annoying bug where > after running the classifier (Ctrl+Shift+T), the pencil tool sometimes > stops being able to paint lines until you click (or Alt+Tab) away from the > Labkit window and then back. > > 2. Export probability map to ImageJ > > This gets you back to a regular image window, which you can then manipulate > with other plugins. > > You might always want to save this image to a TIFF file now, since it will > serve as a good starting point for further experimentation. > > 3. Smooth the image to reduce noise. I used the Kuwahara filter. But it > didn't want to run on a 32-bit multichannel image, so I had to first run > Image > Type > 8-bit and then Duplicate only the first slice of the image. > > The easiest way to run it is to type "kuwa" into the search bar of Fiji. > > After running this filter with a smoothing window of 5, my image looked > like this: > > [image: smoothed-small.png] > > 4. Do the actual segmentation with the Morphological Segmentation plugin, > part of MorphoLibJ. https://imagej.net/plugins/morpholibj > > For this plugin you will need to enable the IJPB-plugins update site via > Help > Update..., "Manage Update Sites" button, in Fiji. > > I left the input image as Border Image, changed Tolerance to 30, clicked > Run, and then changed the Results Display to "Catchment basins". Here is > what that looked like: > > [image: morpholibj-small.png] > > As you can see, it erroneously bisected two of the regions on the bottom > half, as well as one on the top half, but it got most of then right. > > 5. You could then click "Create image" to make another image and measure > the number of pixels of each color to get the size of each region. And > filter out results that aren't close to the expected size, or aren't at the > correct (X,Y) coordinates to be one of the petal shapes. > > I would also suggest to give CellPose a try—I did not try it, but it does > very well on a wide variety of input images. > > You might get better answers on https://forum.image.sc rather than here, > since the state-of-the-art for segmenting scientific images has changed a > lot in recent years and there are many more powerful tools than classical > ImageJ-based segmentation now. > > Regards, > Curtis > > -- > Curtis Rueden > Software architect, LOCI/Eliceiri lab - https://uw-loci.github.io/ > ImageJ2 lead, Fiji maintainer - https://imagej.net/people/ctrueden > Have you tried the Image.sc Forum? https://forum.image.sc/ > > > On Fri, Mar 8, 2024 at 1:48 AM anusuya pal <[email protected]> wrote: > > > Dear all, > > > > I want to measure the area of the flower-like patterns as shown in the > > image. I can do it manually, but I have more than 50 images. Do you have > > any suggestions for doing it automatically? > > > > Thanks for your help, > > Anu > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
