March 9th-10th and 14th 2023
10:00 - 17:00 BST (09:00 - 16:00 UTC)
Instructors: David Pérez-Suárez, Mary Tziraki, Thomas Veale, Gerold Baier, Saba Ferdous, Adam Lee
Helpers: TBC
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UCL's DaSH workshops (based in Software Carpentry) aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, data management, task automation and medical imaging processing. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Where: TR7. 2nd floor, 7 Queen Square, London. Get directions with OpenStreetMap or Google Maps.
When: March 9th-10th and 14th 2023. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).
Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email arc-teaching+carpentries@ucl.ac.uk or m.tziraki@ucl.ac.uk for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Please be sure to complete these surveys before and after the workshop.
| 09:00 | Drop-in session: A clinic to assist with the setup of your computer. We strongly recommend you complete the setup session and have your computer ready for the lesson. |
| 10:00 | Building Programs with Python |
| 11:30 | Morning break |
| 12:00 | Building Programs with Python (Continued) |
| 13:00 | Lunch break |
| 14:00 | Building Programs with Python (Continued) |
| 15:30 | Afternoon break |
| 16:00 | Building Programs with Python (Continued) |
| 17:00 | Wrap-up |
| 09:00 | Drop-in session: A clinic to assist with the setup of your computer. We strongly recommend you complete the setup session and have your computer ready for the lesson. |
| 10:00 | Introduction to 2D and 3D Image Analysis |
| 11:00 | Medical Images from the Scanner to computer |
| 11:30 | Morning break |
| 12:00 | MRI modalities (Continued) |
| 12:30 | Introduction to registration |
| 13:00 | Lunch break |
| 14:00 | Structural MRI (sMRI) |
| 15:30 | Afternoon break |
| 16:00 | sMRI: Segmentation and Parcellation |
| 16:20 | sMRI: Quality control |
| 16:45 | Statistical analysis and reproducibility |
| 17:00 | Wrap-up |
| 09:00 | Drop-in session |
| 10:00 | Analysing microscopic data |
| 11:30 | Morning break |
| 12:00 | Analysing microscopic data (Continued) |
| 13:00 | Lunch break |
| 14:00 | Cell segmentation |
| 15:30 | Afternoon break |
| 16:00 | Clustering Images |
| 17:00 | Wrap-up |
To participate in a UCL DaSH workshop, you will need access to software as described on the setup page. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).
We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).
bash Anaconda3-and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
yes and press enter to approve the license.
Press Enter (or Return)
to approve the default location
for the files.
Type yes and press
Enter (or Return)
to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).