Hello All,
I am working on a project in which I need to estimate the amount of cells in a whole specimen.
I am able to create a grid. I have the cell counts for random point within the grid, however I need to calculate the area within each grid. This is especially challenging within grids that are on the borders. I would like to also have the area data summarized in an excel… What is the best way to approach this?
Thank you
Do you have an example image? It would be easier to advise with more information. Not really sure how you are generating your tiles.
QuPath can create tiles of a set size as restricted by another object, if you have a tissue outline.
What you are suggesting would be perfect!.. how did you do that?
Is the outline something I would generate on ImageJ and import?
Using QuPath, it is intended for analysis of whole slide images. Depending on how easy it is to segment your cells, it may be easier to just calculate the whole thing. Take a look:
Youtube IHC analysis
User guide for getting started
QuPath wiki
Also, each tile can be processed through a basic ImageJ script, though QuPath’s version of ImageJ is fairly old. Alternatively you can export tiles in other ways as their own individual images, but I’m not great at that and you might be better off checking elsewhere in the forum/issues page for examples.
Specifically for that, though, I used Analyze->Preprocessing->Simple tissue detection followed by Analyze->Region Identification->Tiles and superpixels->Create tiles
There is more on both of those functions in the user guide.
