Building the Jupyter Community in MSK Imaging Research

A Jupyter Community Workshop organized by and for the Open and Reproducible Musculoskeletal Imaging Research (ORMIR) Community

Sponsored by NumFOCUS and financially supported by Bloomberg and Amazon Web Services

Dates: June 9-11, 2022

Venue: The Student Hotel (now The Social Hub), Sphinxcour 9A, 6211XZ Maastricht, The Netherlands

In this page, you will find:

Aims and GitHub repositories at these links:
- Ciclope: aims, GitHub repository
- Bone erosion: aims
- Muscle BIDS: aims, GitHub repository
Please follow the coding guidelines!

Please, install Anaconda before the workshop!
Intro to the Jupyter ecosystem and Python and Second layer analysis: Pandas and Matplotlib
- Instructor: Serena Bonaretti
- Material: here
First layer analysis: ITK
- Instructors: Dženan Zukić and Jared Vicory
- Aims: here
- Material: here

Members of the community who cannot join - We will miss you!

Public transportation in The Netherlands is very reliable
If you travel nationally, you can schedule your trip at ns.nl
If you travel internationally (e.g. from/to Brussels airport), you can schedule your trip at nsinternational.com
Recommendations:
- At Amsterdam Schipol International Airport, train tracks are at the airport hall. You do not need to leave the airport building. Buy the ticket in the hall, go downstairs to the tracks, and enjoy the trip!
- From Amsterdam Schipol International Airport to Maastricht: The trip takes about 2h45'. Consider transfering in Utrecht or 'S-Hertogenbosch (not Amsterdam). Important: Sit in the front of the train. Sometimes (mainly late at night) the train splits in 2 parts in Eindhoven. The head of the train goes to Maastricht, and the tail of the train goes to Venlo. They communicate the split on the train, but it often is only in Dutch
- From Maastricht train station to The Student Hotel:
  - By bus: Outside the train station, the bus terminals are on the right. You can buy a ticket on the bus. Several buses go to The Student Hotel and they are very frequent
  - On foot: You can walk through downtown and enjoy the athmosphere!
- How to get to QMSKI: Take the train from Maastricht to Noordwijk. The trip takes about 3h30'. You can plan your trip on ns.nl or Google Maps. If you are on a budget, consider booking a hotel room in Maastricht for Sat/Sun, and then travel on Sunday

Travel reimbursements are only for participants from European, Middle Eastern, and one International institutions. Apologies to the people who come from other continents. The budget for traveling was limited and the criterion was to reimburse as many people as possible
To get a travel reimbursement, there are 2 steps to be done by June 30, 2022:
1. Send Serena an email with the amount you are requesting and a copy of the expense receipts in one single .pdf file
2. Fill out the reimbursement form. Suggestions for some of the questions:
- 1 -> Workshop Name: E: Building the Jupyter community in MSK imaging research
- 4 -> Category Travel
- 7-12 -> Your institution address
Reimbursement guidelines: here

Shop hours: 10am-6pm; Sundays: 12pm-6pm
It might rain: have an umbrella or a raincoat!
Everybody speaks English!
If you want to go out for dinner on Saturday night, consider reserving before. Also, restaurants usually do not accept big groups over the weekend

Enjoy downtown, with its restaurants, shops, ancient walls, squares, and churches
Dominicanen Boekhandel: Gothic cathedral hosting a bookstore and a coffee place
De Bisschopsmolen: Watermill from the 11th century used to grind spelt, which is then used by the backery next door to bake bread, Limburg vlaai, and other delicious products
Maastricht library: Hosting free exhibitions, with a gorgeous view of Maastricht from the 4th floor
Market on Friday: 8:00am - 2:00pm
Ask for more!