Remove changes not related to slides

.gitignore

@@ -14,3 +14,7 @@
 _site/ 
 Gemfile.lock
 
+## Kvasir-SEG dataset
+kvasir-seg.zip
+Kvasir-SEG
+

README.md

@@ -1,4 +1,7 @@
 # :nut_and_bolt: Hacking Real-time AI workflows for Surgery :wrench: 
+![fig](program/figures/team-logo.png)
+
+
 Hackathon hosted by CMIC    
 9-10th November 2023    
 https://cmic-ucl.github.io/CMICHACKS/    
@@ -51,9 +54,12 @@ Registration is free and you can get your tickets [here](https://www.eventbrite.
 The venue of the hackathon is Jeffery (Thursday) and Elvin (Friday) rooms, Level 1, main UCL Institute of Education (IOE) building, 20 Bedford Way, London WC1H 0AL. [google-maps](https://maps.app.goo.gl/XXBmo7E9Zq2CqZ4E6)    
 
 ## :computer: Pre-requisites for participants  
-* Participants require to bring their own computers either with CPU or GPU. Computers with GPU will be idea to prototype models. However, we will also prepare pre-training models and simple AI workflows that does not require GPUs. 
-* Have a Github username. Otherwise, [sign up](https://docs.github.com/en/get-started/signing-up-for-github/signing-up-for-a-new-github-account) to GitHub to create an account.
-* Clone https://github.com/SciKit-Surgery/cmicHACKS2.git  
+* Participants require to bring their own computers either with CPU or GPU. Computers with GPU will be ideal to prototype models. However, we will also prepare simple AI workflows in google-colabs that does not require GPUs. 
+* Gmail account to prototype models in google colabs.   
+* Github username. Otherwise, [sign up](https://docs.github.com/en/get-started/signing-up-for-github/signing-up-for-a-new-github-account) to GitHub to create an account.
+* Clone https://github.com/SciKit-Surgery/cmicHACKS2.git. 
+See further details here [:link:](program/day-one/README.md#1100--1200--intro-and-preparations-to-hack) 
+
 
 ## :family: Forum
 We are using [Discussions](https://github.com/SciKit-Surgery/cmicHACKS2/discussions/) as a place to connect with other members of our community.

program/day-one/README.md

@@ -3,10 +3,12 @@
 ## 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. Setup your [Personal Access Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens)
+1. Generate your SSH keys as suggested [here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent) (or [here](https://github.com/mxochicale/tools/blob/main/github/SSH.md))  
+1.1 Alternatively you can setup your [Personal Access Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens)
 2. Clone repo
 ```
-git clone https://github.com/SciKit-Surgery/cmicHACKS2.git 
+git clone https://github.com/SciKit-Surgery/cmicHACKS2.git  ##using HTTPS
+git clone [email protected]:SciKit-Surgery/cmicHACKS2.git   ##using password-protected SSH key
 ```
 3. Workflow for issue management 
 ```mermaid
@@ -55,19 +57,12 @@ IEEE Access. 2021 Mar 4;9:40496-40510. doi: 10.1109/ACCESS.2021.3063716. PMID: 3
 [google-citations](https://scholar.google.com/scholar?cites=11882550127852592683&as_sdt=2005&sciodt=0,5&hl=en)
 
 
-Lee, Ji Young, Jinhoon Jeong, Eun Mi Song, Chunae Ha, Hyo Jeong Lee, Ja Eun Koo, Dong-Hoon Yang, Namkug Kim, and Jeong-Sik Byeon. 
-"Real-time detection of colon polyps during colonoscopy using deep learning: systematic validation with four independent datasets." 
-Scientific reports 10, no. 1 (2020): 8379.
-[google-citations](https://scholar.google.com/scholar?cites=6958241942401260456&as_sdt=2005&sciodt=0,5&hl=en)
+"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/ 
 
-Nogueira-Rodríguez, Alba, Rubén Domínguez-Carbajales, Fernando Campos-Tato, Jesus Herrero, Manuel Puga, David Remedios, Laura Rivas et al. 
-"Real-time polyp detection model using convolutional neural networks." 
-Neural Computing and Applications 34, no. 13 (2022): 10375-10396.
-[google-citations](https://scholar.google.com/scholar?cites=10921968363398150924&as_sdt=2005&sciodt=0,5&hl=en)
 
-
-
-Label tools:   
+Labelling tools:   
 * https://www.robots.ox.ac.uk/~vgg/software/via/  
 * https://labelstud.io/  
 * https://github.com/wkentaro/labelme