35 - Cell Nuclei analysis in Python using watershed segmentation

This tutorial explains the process of cell nuclei segmentation followed by counting and sizing the nuclei. The results are exported into a csv file for further analysis. The tutorial is a follow up to the previous 3 videos in this playlist where grain segmentation was performed using traditional and watershed segmentation, respectively. The video is dedicated to all biologists who are wasting their valuable research time in doing these task manually!

[Sinanmmd]

This analysis will help me in my PhD, I have used a software but I want thinking to make my own setup in order to have skills and know what I am doing in practice. Thank you Professor.

[tailises]

Please continue this amazing job! Your tutorials are great!

[ADPathos]

This was far more useful to me than the openCV tutorial. Thanks!

[felip]

Quite amazing seeing that the program you wrote works for other things too!

[gye]

Glad to see some similar/related thing I did in my lab.

[guyhadary]

Hi, Great tutorial, thank you for that.
It worked perfectly for 1 full folder of images and count the cells perfectly (after few adjustments). But when I tried it on different folder the counting wasn't good.
Many cells with weak fluorescence weren't including in the counting, I tried to play with the threshold but couldn't change the counting result.
Any suggestions could really help my project.

Thank you.

[Renardbardhi]

Amazing job indeed. I just want to ask how can I increase the tension of the yellow color that surrounds the cells. To be more intense.

[univweb]

hello sir, i am on nuclei segmentation and i need some datasets to work with, please do you have any idea howa can i get segmentation datasets such as TCGA ...

[jamilal-idrus]

excuse me sir, i am always follow your another tutorial, but in this tutorial... how can i show my final watershed image in google colab?

[asmabenbrahem]

Can you please answer this question: why distance transform is better than erosion ? you said that erosion will eliminate the tiny cells, but setting a big factor (a.k.a factor*max (distance_transform)) will also elminate this tiny cells. Can you please provide me with a good explanation or a link with trusted information ?

[sciencelogs]

As much as I have tried, I have not been able to do the watershed on a single-channel grayscale image. Any solution for it. Your help would be greatly appreciated

[nying]

Sir, can I used this sure-foreground method in my paper to publish? Your idea is excellent. I want to cite this to avoid the academic ethic, but this is the YouTube channels. Therefore, I can't add this YouTube link in my paper according to the Journel demand.

[amarug]

awesome tutorial and i really like your attitude!

[TDAnyadubaMScPhD]

This is so great! Please I have a question, I have droplets with particles inside them, how do I apply this to count the number of particles inside each droplet. Basically I need to know, area of droplet and the number of particles inside it

[ramchandracheke]

First I like your videos then watch it !

[krisbramleydrums]

Hi Sreeni, thanks so much for doing these videos, they are keeping me sane during Covid lockdown! Quick question: is there a way to automatically count the number of cells in the image following the watershed segmentation?

[pareshpriyadarshanrana]

Can you please tell about how to know which color in img2 corresponds to which label of "regions" while extracting information. Also, can we number label these nuclei in python the way ROIs are labelled in ImageJ?

[BrunoGocan]

What is, if there is any, the relation between k-means cluster and watershed segmentation?

[mahhhhh]

Hi professor. I'm doing cnn for stem cell for my final year project. But I want to know, how to train the system, since it has no memory or cannot identify which is which type of stem cell. I have CFU GM, M and G. I don't have the idea of what to do for segmentation because all the cell looks same. Can u give me some advice, on how I should process my data

[hajobarolachattujje]

can you share how to do watershed segmentation of cell boundaries with the same osteosarcoma image?