Thank you for making the video. I don't quite get what is measuring after 1:00. What are the orange color labeling? The invasive cells? Which parameter should I use? Count, size, %area, perim?
After minute th-cam.com/video/H5cj2wBT59A/w-d-xo.html, it measures the number of particles (in this case). However, In the spheroid case, you are only interested in the area of the main "particle" which is the spheroid itself. Alternatively just copy the total area in the summary of results window.
Thank you very much for this video. I can see visually that my spheroids treated with the highest concentration show a larger halo of detached cells than the untreated ones. However, I'm having trouble quantifying this difference or delimiting the second halo. Do you have any tips? Thanks again for all your videos !
Hi! a very informative video. I would like to know if there's a way to do a densitometric analysis which would showcase the clustering ability of the cells. thanks!
@@bioinfotips I'm working with cells overexpressed with a certain protein which makes them cluster more than the control cells. From visual interpretation I can tell my protein of interest is resulting in a higher cell-cell adhesion. So my question is, how do I quantify that? The control cells have many blank spaces in between which the mutant doesn't have
In that case, I think you can try to measure the area of the sferoid with the wand tool, so it quantifies all the continuous area, after thresholding the image. Just make sure you use the same threshold value for every image. Let me know if that works.
Hi, thank you for making the video. After I have obtained the area, length, etc., how do I apply the formula to measure volume? V=4/3 pi *r 3. I mean: what is the r? Thanks in advance!
Hi :) the r is the lenght divided by 2. But keep in mind that the spheroids are not perfect circles for the length can change dependending on how you are measuring it.
@@bioinfotips Thank you for your answer!! In a paper they describe r as: "the mean of the long diameter and the short diameter of the spheroid divided by two". Does this mean that I should consider the short and long length and average these two values, then divide it by 2, and raise it to the third? Sorry for these basic questions, but I’m having a bit of trouble at the moment. Thanks in advance.
@@ilariaserra5563 Yes that is probably the best approach! Just take the diameter in the highest point and lowest point, sum then and divide by 2, so you have the average diameter. After that, divide by 2 again and you have your average radius, that you can use in the volume fórmula. Hope this helped.
Hello I have a question, can you please help me? I want to count the number of hair grafts inside the plate, what software do you recommend? I have used the Fiji software (filament detector, but I have not received the correct answer) Can you please guide me?( may I have your email to send you the photos?)
Thank you for your comment. Instead of starting by making the image an 8 bit, try to go to "process" and then "binary" and "make binary". Let me know if it's still in reversed colors.
Thank you for making the video. I don't quite get what is measuring after 1:00. What are the orange color labeling? The invasive cells? Which parameter should I use? Count, size, %area, perim?
After minute th-cam.com/video/H5cj2wBT59A/w-d-xo.html, it measures the number of particles (in this case). However, In the spheroid case, you are only interested in the area of the main "particle" which is the spheroid itself. Alternatively just copy the total area in the summary of results window.
Thank you very much for this video. I can see visually that my spheroids treated with the highest concentration show a larger halo of detached cells than the untreated ones. However, I'm having trouble quantifying this difference or delimiting the second halo. Do you have any tips? Thanks again for all your videos !
Hi :) have you try to increase the contrast?
Hi! great video, do you have a tip for meassuring the area of cell migration of the spheroids?
Hi Juan. You mean like expansion of the spheroids? If that's the case, probably measuring the area before and after the cell migration should do it.
Hi! a very informative video. I would like to know if there's a way to do a densitometric analysis which would showcase the clustering ability of the cells. thanks!
Hi. Thank you. You mean the pixel density?
@@bioinfotips I'm working with cells overexpressed with a certain protein which makes them cluster more than the control cells. From visual interpretation I can tell my protein of interest is resulting in a higher cell-cell adhesion. So my question is, how do I quantify that? The control cells have many blank spaces in between which the mutant doesn't have
In that case, I think you can try to measure the area of the sferoid with the wand tool, so it quantifies all the continuous area, after thresholding the image. Just make sure you use the same threshold value for every image. Let me know if that works.
@@bioinfotips thanks!! This helps. Got what I wanted and glad to see my hypothesis is working. Have a great day ahead!
Hi, thank you for making the video. After I have obtained the area, length, etc., how do I apply the formula to measure volume? V=4/3 pi *r 3. I mean: what is the r? Thanks in advance!
Hi :) the r is the lenght divided by 2. But keep in mind that the spheroids are not perfect circles for the length can change dependending on how you are measuring it.
@@bioinfotips Thank you for your answer!! In a paper they describe r as: "the mean of the long diameter and the short diameter of the spheroid divided by two". Does this mean that I should consider the short and long length and average these two values, then divide it by 2, and raise it to the third?
Sorry for these basic questions, but I’m having a bit of trouble at the moment. Thanks in advance.
@@ilariaserra5563 Yes that is probably the best approach! Just take the diameter in the highest point and lowest point, sum then and divide by 2, so you have the average diameter. After that, divide by 2 again and you have your average radius, that you can use in the volume fórmula. Hope this helped.
@@bioinfotips Definitely, thank you very much!
@@ilariaserra5563 Glad I could help :)
i don't know why but when i make it binary, my spheroid turns white and the background black...
Hello Bandit. The color itself is not relevant. Are you able to quantify correctly the area of the spheroid with the wand tool?
that's the problem, the area is not accurate and i don't know what to do
maybe is an error of some sort..
(also didn't expect a response, thank you!!)
If you want you can send it to me so I can take a look. bioinfotips@gmail.com
Hello
I have a question, can you please help me?
I want to count the number of hair grafts inside the plate, what software do you recommend?
I have used the Fiji software (filament detector, but I have not received the correct answer)
Can you please guide me?( may I have your email to send you the photos?)
Sure send me the email
@@bioinfotips I do not find your Email.😅
My bad. I thought you had sent a previous one: bioinfotips@gmail.com
similar to the above comment, when I made it binary my spheroid and some other areas of the image go white and background black
Thank you for your comment. Instead of starting by making the image an 8 bit, try to go to "process" and then "binary" and "make binary". Let me know if it's still in reversed colors.