Hi, thank you for your video. It is very use for me. I have a quesqion, I use this plugin but it is too slow. How I can increase and optimize the speed? I tried changing the options, but it was impossible.
Hi! If after edge detection, thresholding, and binary erosion, the process to detect circles is slow, you might want to try downscaling your image first. You might want to try preprocessing your image (e.g. background subtraction or noise filtering) before edge detection.
@@johanna.m.dela-cruz Thanks for the quick response. My images are not complicated, but it's so hard to find the correct conditions for analysis. The software keeps freezing ;o;
Hi there! If you are able to threshold your image, you can just do Particle analysis (Analyze Particles command) and limit detection based on circularity (0-1, with 1 being a circle).
I have an image sequence of about 40 pictures. The picture is 5 droplets wetting out on a surface (top view). Pictures were taken every 5 seconds. I want to measure the change in diameter(or area, I can back calculate the diameter) as the droplet wets out. I tried using the Hough circle transform like you explained in your video. It worked, but the results table only shows the radius for the 5 droplets in the one mask that was created. Is there an easy way to create masks for all the images in the sequence? Or is there a better way of doing this? Thank you in advance.
@@marulez7 Hi there. It might be easier to advise you if I can see a representative image. Classic Thresholding does not always work. It depends on the image. Perhaps it would be better if you send me an email so we can discuss this further. Thanks for watching my video.
@@johanna.m.dela-cruz Thank you for your response. I figured out how to create a mask for a whole image sequence. instead of doing Edit> Select> Create Mask, you do Process > Binary > Convert to Mask. Sadly, I can't send you pictures due to protprietary information, but I appreciate you trying to help.
![FIJI (ImageJ): Counting Foci or Puncta [Difference of Gaussians]](http://i.ytimg.com/vi/5z-BhcpiXp0/mqdefault.jpg)
![FIJI (ImageJ): Fiber Orientation and Direction [Directionality & OrientationJ]](/img/n.gif)
Hi, when I press the help button to install the UCB plugin there is no 'update' option. can I find this plugin in the Dev. resources option
Hi Erin. Try typing update in the search bar….By the way, you are using Fiji, right?
Hi, thank you for your video. It is very use for me. I have a quesqion, I use this plugin but it is too slow. How I can increase and optimize the speed? I tried changing the options, but it was impossible.
Hi! If after edge detection, thresholding, and binary erosion, the process to detect circles is slow, you might want to try downscaling your image first. You might want to try preprocessing your image (e.g. background subtraction or noise filtering) before edge detection.
@@johanna.m.dela-cruz Thanks for the quick response. My images are not complicated, but it's so hard to find the correct conditions for analysis. The software keeps freezing ;o;
@@jd9611 are you getting out of memory errors? If not, just try a smaller image size if HCT works…
@@johanna.m.dela-cruz Too slow and running out of memory. When I Change the options, the circles being measured, but it's still slow.
HI, is there any hough transform to detect ellipse? Or any macro code which can be run to detect ellipse.
Hi there! If you are able to threshold your image, you can just do Particle analysis (Analyze Particles command) and limit detection based on circularity (0-1, with 1 being a circle).
Thank you.
how do you create a mask of an image sequence?
I have an image sequence of about 40 pictures. The picture is 5 droplets wetting out on a surface (top view). Pictures were taken every 5 seconds. I want to measure the change in diameter(or area, I can back calculate the diameter) as the droplet wets out. I tried using the Hough circle transform like you explained in your video. It worked, but the results table only shows the radius for the 5 droplets in the one mask that was created. Is there an easy way to create masks for all the images in the sequence? Or is there a better way of doing this?
Thank you in advance.
@@marulez7 Hi there. It might be easier to advise you if I can see a representative image. Classic Thresholding does not always work. It depends on the image. Perhaps it would be better if you send me an email so we can discuss this further. Thanks for watching my video.
@@johanna.m.dela-cruz Thank you for your response. I figured out how to create a mask for a whole image sequence. instead of doing Edit> Select> Create Mask, you do Process > Binary > Convert to Mask. Sadly, I can't send you pictures due to protprietary information, but I appreciate you trying to help.
No problem. And yes, you can convert your stack to a mask or make binary that way. I wasn’t sure if classic thresholding works with your images.