# DaSH IDEAS L2D workshop In Python and Medical Image Analysis
# March 9th, 10th, 14th 2023

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### About the workshop

It is an in-person workshop and it will take place at room TR7 on the 2nd floor of the 7 Queen Square London

Check the [schedule of the workshop for every day](https://github-pages.ucl.ac.uk/2023-03-09-UCL-DasH/#schedule).

You are advised to bring your laptops and try to set it up for the first day that we will the Anaconda Navigator.
Instructions are from **[the Python Lesson]( https://swcarpentry.github.io/python-novice-gapminder/setup.html)**.

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### About this document
This document is synchronized as you type so that everyone viewing this page sees the same text. This allows you to collaborate seamlessly on documents. To Edit click on the :pencil2: icon on the top left. However, we don't want you to edit this one. You can create another one and share it with your teammates.

**Use of this service is restricted to members of The IDEAS and L2D**; this is not for general purpose use (for that, try etherpad.wikimedia.org).

Users are expected to follow our **[Code of Conduct](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html)**.

All content is publicly available under the [Creative Commons Attribution License](https://creativecommons.org/licenses/by/4.0/).

General questions or feedback? Contact Mary Tziraki [[e-mail]] and Tom Veale, [[e-mail]].
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## Please check this HackMD document every day for updates and the resources we will share with you

1) Please fill out **[the preworkshop feedback form here](https://forms.office.com/Pages/DesignPageV2.aspx?subpage=design&FormId=_oivH5ipW0yTySEKEdmlwlkwR0NSRchAsbK2z6L_MPlURUcwNENJNkVDOEFLQUFNUFAxU1ZaMTdOUS4u&Token=de3522fc03d04592a37f1120a2462852)**
2) For those unfamiliar with The Unix Shell, or command line, please read the pdf file with my presentation on teh Unix Shell that I've sent you to the welcomming email.
I had create a video where I'm walking you throu all the commands, however due to technical issues I cannot share it for the momment.
3) For the first day, we will follow **[the lesson on Python from the Software Carpentries site](https://swcarpentry.github.io/python-novice-gapminder/)**. If you want you could look at it and try the first two episodes, but it is not nessassary as we will teach you tommoro
4) If you don't have GitHub You'll need [to create an account on GitHub](https://github.com/signup) and install the [GitHub CLI tool](https://cli.github.com).

## Set up your machines
a) For tomorrow (9th of March), you will need the instructions for setting up Anaconda navigator from **[the Python Lesson]( https://swcarpentry.github.io/python-novice-gapminder/setup.html)**.
b) Later today or mommorow, we will update the dependencies you will need for Day 2 and Day 3. Please check this HackMD page. **[Libraries set-up instuctions](https://github-pages.ucl.ac.uk/2023-03-09-UCL-DasH/setup/)**

c) If you experience issues with your machines, e strongly recommend attending the set-up sessions between 9:00am-10:00am that we hold every day,

## To install the dependencies will appear below, please keep on checking this document for updates.
**[Libraries set-up instuctions](https://github-pages.ucl.ac.uk/2023-03-09-UCL-DasH/setup/)**

The installation scripts can be downloaded from [here](https://liveuclac-my.sharepoint.com/:u:/g/personal/skgttdv_ucl_ac_uk/EV7K_QprfY5PrxwbI-w0X94BAr-ck2BwpCBH1cr8IBxBmA?e=LE7Qb1)

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## 9th March - IDEAS Day- Python course

1. The **[Python Lesson is here]( https://swcarpentry.github.io/python-novice-gapminder/setup.html)**. We will work with you using exercise notebooks and we hope you will save them and study them following the instructions in the lesson above.

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## 10th March - IDEAS Day- Medical Image Analysis-MRI

1. Please download the notebooks and data needed for today. The link to download the data is **[here](https://liveuclac-my.sharepoint.com/:u:/g/personal/skgttdv_ucl_ac_uk/EdIbskvnD29IhOP5GpPIzbwBT9INPp0iUReUWgc7pjN0Sw?e=gYWo4Y)** (~450MB). The `Download` button is in the top left corner of the screen.
3. If you are unable to download the files - ask Tom for a USB stick to transfer the files over to your machine.
4. Please navigate to the `exercise_books/` directory. We will be using the jupyter notebooks in here for today's session.
5. All the complete notebooks with the code and the exercises are in the `code` directory. You are not expected to know them but use them as reference, if ever need any of their codes.
6. We gave you lots of materials that we were not intended to cover in one day. We have covered notebooks 1, 2, part of 3, 5, and 6.

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## 14th of March Learn to Discover (L2D) Day
1) Please follow the **[set-up page for L2D](https://learntodiscover.github.io/Carpentries_ImageAnalysis/index.html)**, and download **ONLY THE DATASET** you will find at the end of the page.

You will work on an emply Jupyter Notebook

2) The whole lesson in **[Microscopic Image Analysis is here](https://learntodiscover.github.io/Carpentries_ImageAnalysis/01-section1.html)**

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