Calculate the area of the cells

Python
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20191115_EBs_4X_Crtl2_Day4_P1
20191115_EBs_4X_Crtl2_Day4_P11600Ă—1200 389 KB

Calculate the area of the cells (big circles)

Thank you,

Timothy Tax

2

You can talk to ChatGPT like that but not to other humans.

You should elaborate. Who is giving you this assignment? Of what value is the solution to that individual? Of what value is the solution to you? What research have you done? Show your work.

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I apologize crackwitz, this assignment was given to me by a post doc in my research lab, and I am open to collaborate with others in optimizing a solution. The surface areas are typically calculated manually and are prevalent to a very long winded neuroscientific experiment involving testing veraguamides on mouse DRG neurons. I know OpenCV can be used here, but whenever I try to apply thresholding and detect cells I am not able to due to my lack of experience with OpenCV.

Best,

Timothy Tax

5

I would recommend applying a neural network for semantic segmentation. that should be trained to distinguish “cell” vs “background”.

then you’ll have a segmentation mask and you can just count the pixels for area.

for training, you would paint the inside of many cells. just the insides because you’ll be sure of the classification for those pixels. you would also paint areas that are clearly background.

you would leave pixels near edges unpainted (“unsure”). those represent leeway for the model, and human uncertainty.

precise annotation is a lot of manual effort. small mistakes in the ground truth can greatly diminish the model’s performance. that’s why your training should have these “sure foreground” and “sure background” masks, and not reward or punish the model for any classification in the unsure areas.

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