Cannot find 'logs' folder

[Shawnmhy]

Hi, I tried to install the package as instructed. When I run the command 'pythion setup.py install', I got a warning saying that WARNING:root:Fail load requirements file, so using default ones." Seems like there is no error message, however, I couldn't find the 'logs' folder to load the model. Please advise how to solve this issue, thank you so much!

[YubinXie]

Hi @Shawnmhy , the model is available with the link in the readme page of the GitHub.

[Shawnmhy]

Hi Yubin, thank you for the prompt response. Now I can see the model and successfully loaded into my work. In addition, I am also wondering if the pretrained model can work with grayscale images? If so, how should I make the change? I tried simply to stack my 2D grayscale image into a 3D pseudo RGB image (all layers have the same value) and seems like the prediction is bad.

[YubinXie]

there is no gray cells in the original training data - that's why you see the prediction blank.

if your grayscale image is a staining of DAPI, make it a blue RGB image. if it is a tumor/cell membrane marker, make it a red RGB images. this should work for you.

[Shawnmhy]

Thank you Yubin, by blue RGB you mean a 3D numpy array with R and G channels are all zero and only B channel corresponds to the grayscale array, is that correct?

[YubinXie]

yes

[Shawnmhy]

Thank you so much!