Image pre-processing

[YassineElbouchaibi]

Hey,

Sorry to ask such a silly question but could you help me with my images pre-processing to use your model and weights

Here is what I did :

1. I downloaded the CVC-ClinicDB dataset. (images and masks are in tiff format)
2. I cloned your repo and added your weights to ./files/

3. I changed your data.py -> main() to the following :

   def main():
   np.random.seed(42)
   path = "../CVC-ClinicDB/"
   test_x = glob(os.path.join(path, "Original/*"))
   test_y = glob(os.path.join(path, "Ground Truth/*"))
   
   create_dir("new_data/test/image/")
   create_dir("new_data/test/mask/")
   
   augment_data(test_x, test_y, "new_data/test/", augment=False)

   At this point I had 2 folders with images in JPEG (.jpg) format but when I run the prediction, I get results like this :

When I do the same with ETIS-LaribPolypDB dataset, I get results like these :

Do you know what I'm doing wrong? Do you have any code examples to process an image and run a prediction? Or do you have a pre-processed image dataset?

FYI: I'm working on a school project where I want to use your model and weights as a backend and build a web gui to run predictions and have some cool gui features

[YassineElbouchaibi]

Ah, I believe this is because I used the weights for the Lesion Boundary challenge... Would you have weights for MICCAI 2015 Segmentation challenge ?

[DebeshJha]

@YassineElbouchaibi

I have now uploaded the weight file for the CVC-ClinicDB (2015 MICCAI sub-challenge on automatic polyp detection dataset). For the (2015 MICCAI sub-challenge on automatic polyp detection dataset), please test with the ETIS-Larib Dataset. 2015 MICCAI sub-challenge on automatic polyp detection dataset

All the best for your project!

Best regards, Debesh Jha

[YassineElbouchaibi]

@DebeshJha Thanks!! You're amazing!

[YassineElbouchaibi]

@DebeshJha Hey just wanted to give you an update on my school project if you wanted to see the outcome. Its now done. It was made possible by the awesome work you had done here! You can check out a demo here : https://medica-vue.netlify.app/

And the source code here :

• Backend : https://github.com/YassineElbouchaibi/medica-vue-backend
• Frontend : https://github.com/YassineElbouchaibi/medica-vue-frontend

I made sure to mention your projet in the about/credits section of the website!

Thank you!