# EMBL Rome 2023 Pre-workshop session

## Goal: making sure you have all the components you need for the computational session on the 30th June

### 1. Create your working directory:
1. Start `terminal`

2. Copy datas to your own working folder:
- Create your working folder: `mkdir /scratch/[YOUR_initial]/` e.g. `mkdir /scrach/Tong/`
- Copy the tutorial to your working folder: `cp -r /scratch/Tong/* /scratch/[YOUR_initial]/`
- Copy testing notebook to your Desktop: `cp /scratch/[YOUR_initial]/pre-workshop/Testings.ipynb $HOME/Desktop/`

_PS: Unix file system nagivation cheatsheet:_
https://www.codecademy.com/learn/learn-the-command-line/modules/learn-the-command-line-navigation/cheatsheet

### 2. Run testing notebook

1. Open jupyter: `Applications -> Programming -> DL_Course(Pytorch)`
2. Open the testing notebook in jupyter: `Desktop/Testings.ipynb`

3. Run Napari in notebook and play with parameters
- adapted from scikit-image: https://scikit-image.org/docs/stable/user_guide/tutorial_segmentation.html
### 3. Run nf-decoding pipeline
- Enter the folder & run the pipeline
- `cd /scratch/[YOUR_initial]/nf`
- `bash run.sh`
### 4. Bonus:
- https://developmental.cellatlas.io/webatlas