How to use Cellpose? (With Google Colab) – Image Analysis

by





1

I need to “submit a report that recognizes all cells in all sample images of mosquito cells”.

I’ve been investigating and found out that you basically input samples to Cellpose Software, which is for machine learning, and then you can “paint” manually the cells in the image to tell, help or correct the learning model until you create your own model that can recognize the cells by its own with a high rate of success. Then that’s when, I guess, I must input the whole sample images and retrieve the data, layers, in which you can see how the software has separated each cell.

    1. Am I right to this point?? (I guess some terminology is incorrect but if i got the idea thats enough)

Now, also I’ve watched this tutorial https://www.youtube.com/watch?v=5qANHWoubZU
And I see this person explains how to use Cellpose, but she seems to have a red and green channeled samples, which makes it really easy to manipulate and so on.
But the problem is, my Images of cells are much more difficult, they look like whitey-purple, you can tell more or less which cell, but it seems so difficult for the Software, these images look similar to normal maps in videogames. Other images are similar but kinda darker or kinda grayed out (but also, not fully gray)

    1. Is it too much of a problem? Or should I just try the program and paint the cells manually? Should I try to let the Software to try to get all the cells it can and from there human in the loop the result? (I’m asking this while Anaconda installs, it’s taking forever…that’s why I ask before trying myself)

Also, some image samples of the mosquito cells are really difficult to distinguish even for the human eye. I guess I shouldn’t be supposed to know so much biology, so here goes my 3rd question:

    1. Can you guys recommend any subreddit or where to ask about the mosquito cells (how are they supposed to look, what are the white dots in the images, etc.)?

And lastly:

    1. Why do they ask me to submit a report in Google Colab? Is it simply to document the data there better? Does it give extra functionalities when linked to Cellpose?

Thank you so much in advance, any help is really welcomed.



Source link

Leave a Comment