Issue generated patches from MIBI-TOF tiff data

[reemabaskar]

Issue generated patches from MIBI-TOF tiff data

[PENGLU-WashU]

Hello,

Thanks for your interest in our package! Could you please indicate the format of your data? Is it tiff image?

If it is okay, could you please share an image with me so that I can find where the problem is?

Best regards

[reemabaskar]

Hey @PENGLU-WashU! Thank you for your response! Yes they are tiff images that are 1024x1024, and here is also the notebook I used to debug it to this line of code within generate_patches function: patch_collect_sub = self.extract_patches_from_img(Img_DIMR, Row_range, Col_range)
And I have attached 1 FOV as well, thank you so much and looking forward to your reply.

2022-12-03T15-18-19_BIGFISH1_pA_s1_R1C1.zip
IMC_Denoise_Train_and_Predict_MIBIexample.html.zip

[PENGLU-WashU]

Hello! I just checked the images. Are these images the raw files? The images should be denoised before normalization. In that case, the range of the images is beyond [0,1]. Hope these can help.

[reemabaskar]

Hey @PENGLU-WashU ah that's totally fair, it works on raw data! Sorry for my confusion and thank you for your help!