Hello! Thank you very much for this very clear tutorial! I used to do the thresholding manually in ImageJ, but now I want to automate it by linking Ilastik and ImageJ. Do you think it's possible to do it within a macro? if you could help me please ?
I have a macro works for image with single particle for image, it calculate a new circularity parameter. How I can call ROI in the macro, so it will run the function on each particle in the image like it does when you run "`analyze particles" it return the parameters as Area, Perimeter, Circularity and so on? Thanks
Great video! I was wondering if Ilastik can also provide cellular analysis outputs (i.e: cell count, cell size), or does it only output the probability map of cell detection? I am currently trying to find a Fiji plugin that can simultaneously identify and count cells for multiple images at once. I have tried using StarDist, but the ML algorithm is having difficulty differentiating between cell and background. Can Ilastik support this functionality, or is there another Fiji plugin that can do this? I have so many images that individually setting thresholds to count cells would take me years.
Hi, there is an object classifier in Ilastik that will help to split your objects into groups but I think ultimately you only get label maps with predictions so you are left with ImageJ to do the particle analysis. I'd need to read a bit more into it though.
@@CraigDaly any updates on this? I am trying to get axon measurements and maybe soma measurements if i can train it well enough. automation would be very awesome. Working on a macro but it's going slowly atm.
@@maxelsimmel2571 Hi, sorry, I got side tracked with a sabbatical and got involved in a bunch of other stuff - hence no new videos for 11 months. Got an idea for a new series of videos though, but that doesn't help you. It's still on my to do list.
Your is THE BEST CHANNEL on TH-cam!!! Thanks a lot for all the videos you are making!!! 🙏
Thanks, this video is very helpful. How do I then count the cells in image J?
Thank you for the tutorial 👍
Hello! Thank you very much for this very clear tutorial! I used to do the thresholding manually in ImageJ, but now I want to automate it by linking Ilastik and ImageJ. Do you think it's possible to do it within a macro? if you could help me please ?
I have a macro works for image with single particle for image, it calculate a new circularity parameter. How I can call ROI in the macro, so it will run the function on each particle in the image like it does when you run "`analyze particles" it return the parameters as Area, Perimeter, Circularity and so on?
Thanks
Great video! I was wondering if Ilastik can also provide cellular analysis outputs (i.e: cell count, cell size), or does it only output the probability map of cell detection? I am currently trying to find a Fiji plugin that can simultaneously identify and count cells for multiple images at once. I have tried using StarDist, but the ML algorithm is having difficulty differentiating between cell and background. Can Ilastik support this functionality, or is there another Fiji plugin that can do this? I have so many images that individually setting thresholds to count cells would take me years.
Hi, there is an object classifier in Ilastik that will help to split your objects into groups but I think ultimately you only get label maps with predictions so you are left with ImageJ to do the particle analysis. I'd need to read a bit more into it though.
@@CraigDaly any updates on this? I am trying to get axon measurements and maybe soma measurements if i can train it well enough. automation would be very awesome. Working on a macro but it's going slowly atm.
@@maxelsimmel2571 Hi, sorry, I got side tracked with a sabbatical and got involved in a bunch of other stuff - hence no new videos for 11 months. Got an idea for a new series of videos though, but that doesn't help you. It's still on my to do list.