Welcome to the CIL Online Training March 2025. This training course will take place on Tuesday 25th, Wednesday 26th and Thursday 27th March 2025 from 1-5pm UK time.
This document is for participants to find information about the course, ask questions and share answers with each other.
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As participants, you're welcome to contribute to this document by pressing the 'Edit' button at the top of the page. You can edit the text in the left panel and view changes on the right. We'd love to hear from you in the Questions section!
📣 Current activity: Session 1: Welcome.
Learn how to use CIL for standard CT datasets, including analytical reconstruction methods (FBP and FDK), pre-processing techniques, and visualisation tools.
| Time | Topic | Presenter |
|---|---|---|
| 1:00 - 1:10 | Welcome, course overview and icebreaker | Hannah Robarts |
| 1:10 - 2:05 | Session 1: Geometry, data reading and analytical reconstruction 📂 1_Introduction :page_facing_up: 01_intro_walnut_conebeam.ipynb |
Franck Vidal |
| 2:05 - 2:35 | Session 2: Writing your own code in CIL 📂 1_Introduction :open_file_folder: exercises:page_facing_up: 01_intro_seeds_conebeam.ipynb |
Laura Murgatroyd |
| 2:35 - 2:50 | Break | |
| 2:50 - 3:40 | Session 3: Pre-processing 📂 1_Introduction :page_facing_up: 02_intro_sandstone_parallel_roi.ipynb |
Laura Murgatroyd |
| 3:40 - 4:00 | Break | |
| 4:00 - 4:45 | Session 4: Time to explore and discuss 📂 1_Introduction :page_facing_up: 00_CIL_geometry.ipynb:page_facing_up: 03_preprocessing.ipynb:open_file_folder: exercises :page_facing_up: 02_preprocessing_seeds_conebeam.ipynb:page_facing_up: 03_where_is_my_reader.ipynb📂 4_Deep_Dives :page_facing_up: 02_phase_retrieval.ipynb |
Franck Vidal |
| 4:50 - 5:00 | Wrap up and questions | Laura Murgatroyd |
Explore iterative reconstruction methods, going beyond SIRT and CGLS, and incorporating regularisation for improved results.
| Time | Topic | Presenter |
|---|---|---|
| 1:00 - 1:15 | Welcome, intro and cloud setup | Edoardo Pasca |
| 1:15 - 2:15 | Session 1: optimisation 📂 1_Introduction :page_facing_up: 04_FBP_CGLS_SIRT.ipynb:page_facing_up: 05_usb_limited_angle_fbp_sirt.ipynb (extension) |
Edoardo Pasca |
| 2:15 - 2:30 | Break | |
| 2:30 - 3:30 | Session 2: regularisation 📂 binder :page_facing_up: PyData22_deblurring.ipynb📂 2_Iterative :page_facing_up: 01_optimisation_gd_fista.ipynb |
Jakob Sauer Jørgensen |
| 3:30 - 3:45 | Break | |
| 3:45 - 4:45 | Session 3: Time to explore and discuss 📂 2_Iterative :page_facing_up: 05_Laminography_with_TV.ipynb📂 3_Multichannel:page_facing_up: 03_Hyperspectral_reconstruction.ipynb |
Jakob Sauer Jørgensen |
| 4:45 - 5:00 | Wrap-up and questions | Margaret Duff |
Dive into advanced capabilities, including building custom optimisation problems, using callbacks and preconditioners, and creating objective functions.
| Time | Topic | Presenter |
|---|---|---|
| 1:00 - 1:15 | Welcome, intro and cloud setup | |
| 1:15 - 2:30 | Session 1: Building your own optimisation problem using the block framework 📂 2_Iterative :page_facing_up: 02_tikhonov_block_framework.ipynb📂 4_Deep_Dives:page_facing_up: 03_htc_2022.ipynb |
Jakob Sauer Jørgensen |
| 2:30 - 2:45 | Break | |
| 2:45 - 3:30 | Session 2: Customising your optimisation method 📂 4_Deep_Dives:page_facing_up: 01_callbacks.ipynb📂 4_Deep_Dives :page_facing_up: 04_preconditioner_stepsize.ipynb |
Margaret Duff |
| 3:30 - 3:45 | Break | |
| 4:00 - 4:45 | Session 3: Time to explore and discuss 📂 1_Introduction :page_facing_up: 03_where_is_my_reader.ipynb📂 3_Multichannel :page_facing_up: 02_Dynamic_CT.ipynb📂 4_Deep_Dives :page_facing_up: 06_directional_TV.ipynb:page_facing_up: 04_phase_retrieval.ipynb |
|
| 4:45 - 5:00 | Wrap-up, next steps and questions |
- Go to: https://tinyurl.com/cil-online-25 write your name next to a username to claim it for the exercises
- Go to the CIL Jupyter notebook server: https://training.jupyter.stfc.ac.uk/
- Sign up with the username you claimed and a password of your choice. Create a memorable password.
- Then Log in with your username and password
Warning
We can't change your password, so make sure you choose something memorable
We will be using mentimeter for interactive content and feedback, please check here for the link.
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To create a new question, make sure you're in edit mode then type ##### in the relevant section below. A trainer will answer your question in italics
We can support multi-channel images e.g. hyperspectral or dynamic CT, with any number of channels. CIL Data containers have a maximum of 4 dimensions, 3 spatial + 1 channel dimension which could be energy or time, for instance.
We will answer here
Choose a user name from the online form and login as described here.
Get the code
- Find CIL on GitHub https://github.com/tomographicImaging/cil
- Installation instructions: https://github.com/TomographicImaging/CIL?tab=readme-ov-file#installation-of-cil
- Read the documentation: https://tomographicimaging.github.io/CIL/v23.1.0/index.html
Try some examples
- CIL demos: https://github.com/TomographicImaging/CIL-Demos
- CIL User Show-case notebook collection: https://github.com/TomographicImaging/CIL-User-Showcase/
Get support
- Join CIL Discord support platform: https://discord.com/invite/9NTWu9MEGq
- Open an issue in CIL: https://github.com/TomographicImaging/CIL/issues
- Join the CCPi mailing list: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCPI-MEMBERS
- Find out about upcoming events: https://ccpi.ac.uk/
Read some CIL publications
- About CIL https://doi.org/10.1098/rsta.2020.0192
- CIL for multichannel imaging https://doi.org/10.1098/rsta.2020.0193
- Recent paper from the CIL team on a directional reconstruction method (using the PDHG optimization algorithm) for limited-angle CT, which won third prize in the Helsinki Tomography Challenge 2022: https://www.aimsciences.org/article/doi/10.3934/ammc.2023011
Course material
- Slides from today will be emailed to participants