Hi, please forgive me if I'm wrong but in this example you have calculated the number of cells and the area of nuclei, right? But what if I need to calculate stained area (for a given cytoplasmatic marker) and refer it to the number of cells (number of nuclei stained with DAPI)? Thank you.
Hi thanks for the video. I need to count the budding yeast cells. The watershed feature won't nicely distinguish the cells that undergo the budding. Another question is that my cell looks no bigger than yours in this videol, but the area of my cells is 100 times larger
@@nrttaye4033 Thank you very much. I realize that to achieve a good watersheding, I have to have a nice thresholded pictures. I took some DIC pictures for budding yeast cells. The issue is that the interion of the cells are similar in color to the background, so when I do thresholding, the program regarded the cell interion and background the same thing, but the good thing is that the outline of the cells are clear, which can be singled out to form binary picture with cells' outline. But the issue is that some of the outline is open circled as opposed to being a closed circle. Could you please give me some suggestion to work around this issue?
Hello, sure. This might help you out to some extent ruclips.net/video/Tu9UlDspsZM/видео.html In this video, i am measuring the cross section area, however some circles are incomplete. It can be fixed manually. Have a look between 1:30 to 2:15 minutes in the video. Select the same color of your cell outline and close it using the brush tool. All the best
Hello. The color of the nuclei can be converted either into red or B&M. This is the threshold step. Thresholding is the process of converting a color or grayscale image into a binary image. This stage generates a binary image and directs inspection to regions of interest for analysis.
Hello, i am not yet aware of any macros as of now that can measure the length of slightly round/irregular objects (nucleus shape). the closest to any automatic length measure I know is of filaments (ruclips.net/video/CP2A-Jt279c/видео.html) and objects that are strainght and placed in either X or Y axis (ruclips.net/video/Jr2ehzIzoYQ/видео.html). I will get back to you if I come across any macros to measure the cell length automatically.
Hello I have a question I want to count hair graft with imageJ ( i have numbers of grafts but when I use this app the results is not correct ) Would you please help me ?
hello, thanks for reaching out. Does the graft look like hairs with certain length or just transplanted with round shape structures? I may need to know how the transplant images looks like before coming to a conclusion. If they appear like cilia/filament i have video tutorials on how to count these ruclips.net/video/b3Z2t62i9Ds/видео.html if you have overlaps then try "ridge detection" plugin github.com/thorstenwagner/ij-ridgedetection let me know if these helps. Sure happy to help.
Great job man … straight to the point, very helps. 👍🙂
Thank you. Glad you found it useful
Thanks for your great job. But in my case area is differnt but mean intensity are same in a population. So I am worried @@nrttaye4033
Very informative 👍
Nice work!!!
Hi, please forgive me if I'm wrong but in this example you have calculated the number of cells and the area of nuclei, right? But what if I need to calculate stained area (for a given cytoplasmatic marker) and refer it to the number of cells (number of nuclei stained with DAPI)? Thank you.
please see your previous comment for the answer. Thanks for reaching out
@@nrttaye4033 I am also interested in this, would I also be able to get this information? how can I quantify the difference in groups and markers?
Hello please check out this video ruclips.net/video/IQTSsXVOQk0/видео.html let me know if this video answers your query.
Great Video. Do you have any video on measuring CD45 cells in liver by imageJ?
may not be specific to cd45. let me know what type of staining is that for eg IF, IHC etc.
@@nrttaye4033 IHC. Thanks :)
@@nrttaye4033 IHC. Thanks :)
You are welcome. Here are videos for IHC staining ruclips.net/video/K1WKcbKUOMY/видео.html ruclips.net/video/NxNEf1XSPTk/видео.html
Hi thanks for the video. I need to count the budding yeast cells. The watershed feature won't nicely distinguish the cells that undergo the budding. Another question is that my cell looks no bigger than yours in this videol, but the area of my cells is 100 times larger
welcome. to watershed manually, please visit this video ruclips.net/video/P09_sg4yEug/видео.html let me know if this helps
@@nrttaye4033 Thank you very much. I realize that to achieve a good watersheding, I have to have a nice thresholded pictures. I took some DIC pictures for budding yeast cells. The issue is that the interion of the cells are similar in color to the background, so when I do thresholding, the program regarded the cell interion and background the same thing, but the good thing is that the outline of the cells are clear, which can be singled out to form binary picture with cells' outline. But the issue is that some of the outline is open circled as opposed to being a closed circle. Could you please give me some suggestion to work around this issue?
Hello, sure. This might help you out to some extent ruclips.net/video/Tu9UlDspsZM/видео.html In this video, i am measuring the cross section area, however some circles are incomplete. It can be fixed manually. Have a look between 1:30 to 2:15 minutes in the video. Select the same color of your cell outline and close it using the brush tool. All the best
@@nrttaye4033 Thank you very much! really appreciate your help
To measure the fluoresce signal, should I subtract the background first ?
Yes, it is a good idea to subtract background if any. However, it may or may not affect much if the "limit to threshold" is selected.
What is the purpose of the step change the color of nuclear to red?
Hello. The color of the nuclei can be converted either into red or B&M. This is the threshold step. Thresholding is the process of converting a color or grayscale image into a binary image. This stage generates a binary image and directs inspection to regions of interest for analysis.
Help me out to count dual stained cell
Hello, thanks for reaching out. Please visit this video tutorial ruclips.net/video/Z9-Bb68t6ns/видео.html
how do I count the length of the marked cells. I don't want to use the freehand tool since there are too many cells in a frame.
Hello, i am not yet aware of any macros as of now that can measure the length of slightly round/irregular objects (nucleus shape). the closest to any automatic length measure I know is of filaments (ruclips.net/video/CP2A-Jt279c/видео.html) and objects that are strainght and placed in either X or Y axis (ruclips.net/video/Jr2ehzIzoYQ/видео.html). I will get back to you if I come across any macros to measure the cell length automatically.
@@nrttaye4033 thank you so much
Hello I have a question
I want to count hair graft with imageJ
( i have numbers of grafts but when I use this app the results is not correct )
Would you please help me ?
hello, thanks for reaching out. Does the graft look like hairs with certain length or just transplanted with round shape structures? I may need to know how the transplant images looks like before coming to a conclusion. If they appear like cilia/filament i have video tutorials on how to count these ruclips.net/video/b3Z2t62i9Ds/видео.html if you have overlaps then try "ridge detection" plugin github.com/thorstenwagner/ij-ridgedetection let me know if these helps. Sure happy to help.
@@nrttaye4033 hello again , can I send for you one of my plate with specific number of hair graft ?
Can I have your Email address?(for send a image of graft)
here is my email
@@nrttaye4033 thank you .I sent for you an email