- Date: 2021 May 3-5.
- Location: Zoom + SpatialChat.
- Application: (aplication is now closed)
- Any questions? Send an email to Andras Lasso.
- Install 3D Slicer latest stable version (4.11.20210226) -> nightly 64-bit installer. After you installed Slicer, start it, open the Extension manager, and install these extensions: SlicerIGT, SlicerOpenIGTLink, DebuggingTools, SlicerElastix, SegmentRegistration, TCIABrowser, SlicerDMRI, SlicerJupyter.
- Install Git for Windows and TortoiseGit if you have a Windows computer. On macOS and Linux, Git client is usually already installed by default. If you are not comfortable with using softare via the terminal then install a Git client with a graphical user interface, such as GitHub Desktop.
- VisualStudio Code. Install the Python extension from Microsoft (ms-python.python).
- Register a user at www.github.com
- If you want to effectively participate in day 3: get familiar with Python and numpy syntax; spend some time to get to know VTK (read as much of the VTK textbook as you can, try to run some of the VTK examples in Python) and learn about Qt for Python (for example, complete a few basic tutorials).
- Only for students at Queen's: Prepare with a short introduction about yourself (2-3 minutes, supported by 1-2 slides): experience, research interests, something personal
- Install zoom and familiarize yourself with SpatialChat (we will use it for hands-on sessions so that multiple participant can share screen and ask questions from instructors when they get stuck)
- Windows users: Download and install latest stable 64-Bit Plus (2.8.0.20191105-Win64) from here.
- Windows users: Print a set of ArUco markers from here at 100% scale.
- Download NeuroNav tutorial data from here.
The program may slightly change at any time before and during the event, so please check this page regularly. Time zone: UTC-4.
- 9:30 Lab policies, available services, and guides (Tamas, Laura) – only for students at Queen's
zoom - 10:00 Introduction of participants and instructors (all) – only for students at Queen's
zoom - 10:30 Coffee break - bring your own beverage, get to know all the participants
zoom+spatialchat - 11:00 Software platform, open-source, reproducible science (Andras)
zoom - 11:30 Project management (Andras; hands-on, help: Kyle)
zoom+spatialchat - 12:45 Break
- 13:45 3D Slicer basics (Andras; hands-on, help: Kyle, Tamas)
zoom+spatialchat- Overview: core features, community, major extensions (30 min)
- Visualization: load/save, sample data, viewers, models, volume rendering (30 min)
- DICOM (15 min)
- Segmentation (30 min)
- Registration: Elastix, landmark registration, SegmentRegistration, transforms, transform visualization (30 min)
- 16:00 Adjourn
- 9:30 PLUS toolkit main features, writing Plus config files for tracking and image acquisition (Kyle; hands-on, help: Andras)
zoom+spatialchat - 10:30 Sequences, SlicerIGT modules: neuronavigation - coordinate systems, calibrations, visualization (Kyle; hands-on, help: Andras)
zoom+spatialchat - 12:00 Break
- 13:00 Deep learning in Slicer: bone segmentation on ultrasound (create training data, training, inference, volume reconstruction) (Tamas; hands-on)
zoom+spatialchat - 14:45 Break
- 15:00 Deep learning in Slicer: video analysis (annotation, training, using trained network) (Rebecca; hands-on)
zoom+spatialchat - 16:30 Adjourn
- 9:30 Writing correct and understandable code (Andras)
zoom - 10:00 Programming Slicer - part 1: 3D Slicer programming overview (Andras)
zoom - 10:30 Programming Slicer - part 2: Python basics and developing simple example Python module Center of Masses (Kyle, hands-on, help: Andras, Tamas)
zoom+spatialchat - 12:00 Break
- 13:00 Programming Slicer - part 3: Individual work to develop a more advanced module (hands-on, help: Kyle, Andras, Tamas)
zoom+spatialchat - 16:00 Adjourn
Presentation slides and additional files will be available in this repository.