Sample image and/or code
KO stands for Knock out.
STL: Solanum tuberosum lectin
This is part of my final year project, where I am studying breast cancer cells stained in the laboratory and have been studied using confocal microscopy.
My job is to count how many cells they are. So, counting the number of nuclei.
Comment on the shape of the cells- i.e. if they are rounded or elongated.
The images that were provided are two sets of stains, we’ve got the blue stain, the nuclei, and then the same cells have been stained with protein that is labelled green, called a lectin—this stains carbohydrate.
This project’s is to find out if both data set from wild type and knock out in experiment 1 and in experiment 2 shows any changes in the cell shape and type, and how they look morphology and if there is a change in the glycosylation.
I have looked at the resources available from the amazing Image Analysis with ImageJ/FIJI Workshop | 5.17.17 on Vimeo
I am unsure how, to begin with, mine.
- What information are you interested in getting from this image?
I am interested in knowing the number of cells, intensity, shapes, total area, mean, circularity, solidity, and other relevant data that might be helpful., but for now, the mentioned things should suffice.
I would love to create a script so I can do a batch process.
- What stops you from proceeding?
- What have you tried already?
I have done brightness, contrast…
But all of these looked weird to me compared to the desired format. I also have to label it
The above image is a screenshot from a paper that is different from mine, and I have been told it should look like that.
After doing a practice, I got so confused.
Help is much appreciated, and apology for any inconvenient that I have caused.