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Thursday 9th Nov 2023

11:00 -12:00 > Intro and preparations to hack

Hacking: Intro the full AI pipeline and Setting GitHub repository: clone repo, GitHub workflow to code together and document as you hack

  1. Generate your SSH keys as suggested here (or here)
    1.1 Alternatively you can setup your Personal Access Token
  2. Clone repo
git clone https://github.com/SciKit-Surgery/cmicHACKS2.git  ##using HTTPS
git clone [email protected]:SciKit-Surgery/cmicHACKS2.git   ##using password-protected SSH key
  1. Workflow for issue management
  flowchart TD;
      Z[Bug Reported] -->A[...];  
      A[Bug resolution] -->B(Testing OK?);
      B--Yes-->C[Prepare commit];
      B--No-->D[Reopen issue];
      C ----> E[Push Documentation];
      D----> A[Bug resolution];
      E --> F[Close Bug Issue]
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  1. Rebasing your branch with the latest changes of main
git checkout main
git pull origin main
git checkout RB
git rebase main
git push --force origin RB

13:00 - 15:00 > Get familiar with your data

Get familiar with your data (download data, label data, etc.)

fig

  • Kvasir-SEG dataset

The Kvasir-SEG dataset (size 46.2 MB) contains 1000 polyp images and their corresponding ground truth from the Kvasir Dataset v2. The resolution of the images contained in Kvasir-SEG varies from 332x487 to 1920x1072 pixels. The images and its corresponding masks are stored in two separate folders with the same filename. The image files are encoded using JPEG compression, and online browsing is facilitated. The bounding box (coordinate points) for the corresponding images are stored in a JSON file. https://datasets.simula.no/downloads/kvasir-seg.zip

15:15 - 17:00 > Hacking: Training AI workflow

Hacking: Training AI workflow
fig

References

Jha, Debesh, Pia H. Smedsrud, Michael A. Riegler, Pål Halvorsen, Thomas de Lange, Dag Johansen, and Håvard D. Johansen, "Kvasir-seg: A segmented polyp dataset" Proceedings of the International Conference on Multimedia Modeling, pp. 451-462, 2020. google-citations dataset

Jha D, Ali S, Tomar NK, Johansen HD, Johansen D, Rittscher J, Riegler MA, Halvorsen P. Real-Time Polyp Detection, Localization and Segmentation in Colonoscopy Using Deep Learning IEEE Access. 2021 Mar 4;9:40496-40510. doi: 10.1109/ACCESS.2021.3063716. PMID: 33747684; PMCID: PMC7968127. google-citations

Martina, Maria Raffaella, Elisabetta Bianchini, Sara Sinceri, Martina Francesconi, and Vincenzo Gemignani. "Software medical device maintenance: DevOps based approach for problem and modification management." Journal of Software: Evolution and Process (2023): e2570. google-scholar

"Confidently Navigating Software as a Medical Device (SaMD) Product Development" June 15, 2023, Josh Cates, Tim Thirion and Andinet Enquobahrie https://www.kitware.com/confidently-navigating-software-as-a-medical-device-samd-product-development/

Labelling tools:

Other open datasets