Thanks, Brian and Herbie, for your comments. I understand the problem, as the algorithm's success depends on the patterns. I will try to do with what Curtis suggested, as Ankit's suggestion does well in some samples but not all others. If I find trouble and need assistance, I'll turn to the forum for my next question. Anu
On Sat, Mar 9, 2024 at 9:32 PM Brian Northan <[email protected]> wrote: > Hi again > > Herbie says "why then don't we see any results that are fully automatically > obtained from your sample image" > > Curtis's result is almost there, and Curtis suggests "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." > > With a little bit more work I'm confident you could solve the one sample > image by tuning label filter and merge rules, but as I mentioned I'd > hesitate to make conclusions from that one image without being able to test > on a separate 'validation' set, for which we have not trained the pixel > classifier on, or tuned the label modification rules on. > > Brian > > On Sat, Mar 9, 2024 at 7:03 AM Brian Northan <[email protected]> wrote: > > > Hi Anu > > > > There are many similar problems on the Image.sc message board, and both > > classical and advanced AI methods are often shown to be good at solving > the > > one image the researcher shares with the community. What is often > lacking > > is feedback on how the solution(s) suggested, work on the entire set of > > images the researcher needs to process. > > > > I really like Curtis's approach. However the question is how will this > > work on the other 50 or more images? It will depend on the variation in > > the image set. As Herbie points out, we have no idea how Curtis's method > > (or other solution) will work on the entire set. > > > > I hesitate to ask researchers to share more data, as I realize you are > > busy, and you may be constrained as to how much (possibly unpublished) > data > > you are able to release publicly. > > > > However if it is at all possible to share more data (5-10 examples) it > > would really help in assessing whether proposed solutions generalize to > > your entire image set. > > > > At this point I agree that it may be faster to manually do it. However, > > assessing the potential of automation on this problem is still valuable, > > perhaps you will have to do another batch of images in a few months or > > something, and the insights may help others facing similar problems. > > > > Brian > > > > On Sat, Mar 9, 2024 at 6:11 AM Herbie <[email protected]> wrote: > > > >> Greetings Anu, > >> > >> because you called my suggestion as being your "last option" I should > >> like to remark that this idea is exactly *contrary* to what I've > >> suggested. > >> > >> My prognosis is, that you will invest a lot of time with learning and > >> trying various (advanced) approaches and then realize that none of them > >> works fully automatically, i.e. will need additional manual > >> interventions that again take time. In the end you may realize that the > >> better (quicker) approach would have been to start immediately with the > >> manual segmentation of your 50 images. > >> > >> Last but not least, if things would be so easy and economic with using > >> (advanced) approaches, why then don't we see any results that are fully > >> automatically obtained from your sample image? > >> > >> Good luck > >> > >> Herbie > >> > >> :::::::::::::::::::::::::::::::::::::::: > >> Am 08.03.24 um 19:01 schrieb anusuya pal: > >> > 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 > >> > > >> > >> -- > >> 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
