Software Skills for Systems Neuroscience
About us
Neuroinformatics Unit
(Systems) neuroscience & machine learning research software engineering group
Team
What we do
- Data analysis software (anatomy, electrophysiology, functional imaging, behaviour)
- Data management (specifications, tools)
- Collaborations (data science, software development, productionisation)
Current projects
- Data standardisation and management
- Developer tools
- Modelling
- Extracellular electrophysiology analysis
- Video behavioural analysis
- Multiphoton analysis
- Computational neuroanatomy
More details
neuroinformatics.dev
The course
Installation
Installing Python
macOS and Linux
- Open a terminal
- Run the following commands:
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).shWindows
- Download and run the installer from https://github.com/conda-forge/miniforge
- Accept all defaults, BUT make sure to check the box to add Miniforge to your PATH
Set up Git and GitHub
- Follow the installation instructions found at https://git-scm.com/downloads to install Git
- Create a GitHub account at https://github.com
- Install GitHub CLI by following the instructions found at https://cli.github.com/
- Run
gh auth loginto authenticate your GitHub account
Installing an IDE
Follow the instructions found at https://www.jetbrains.com/pycharm/download/ to install PyCharm
Course details
Course schedule
Monday, September 30th - Introduction to Python (1)
Tuesday, October 1st - Data management and sharing (1 & 2)
Wednesday, October 2nd - Introduction to Python (2) & Version control and software development best practices
Thursday, October 3rd - Video behavioural analysis (1 & 2)
Friday, October 4th - Linux and high-performance computing
Monday, October 7th - General microscopy & Histology analysis (1)
Tuesday, October 8th - Histology analysis (2 & 3)
Monday, September 30th
13:00-17:30: Introduction to Python (1)
Aims: Run your first Python script and learn about variables, data types, loops and conditional statements in Python.
Location: SWC Brasserie Seminar Room
Lead by: Sofía Miñano, Igor Tatarnikov, Chang Huan Lo & Adam Tyson
Tuesday, October 1st
9:45-10:45: Data management and sharing (1)
Aims: Motivate the need for good neuroscience data management and introduce current best practices.
Location: SWC Ground Floor Lecture Theatre
Lead by: Joe Ziminski, Niko Sirmpilatze
15:00-17:30: Data management and sharing (2)
Aims: Learn our recommended data organisation principles and supporting software tools.
Location: SWC Ground Floor Lecture Theatre
Lead by: Joe Ziminski, Niko Sirmpilatze
Wednesday, October 2nd
10:00-12:30: Introduction to Python (2)
Aims: Learn how to use third-party Python libraries, work with functions, classes, and objects, and handle exceptions in Python.
Location: GCNU Seminar Room
Lead by: Sofía Miñano, Igor Tatarnikov, Chang Huan Lo & Adam Tyson
13:30-17:30: Version control and software development best practices
Aims: Learn how to keep track of changes to your code with Git and GitHub, work with others on code, and get an initial idea of how structure, document and test your code.
Location: GCNU Seminar Room
Lead by: Alessandro Felder, Laura Porta, Steve Lenzi
Thursday, October 3rd
10:00-13:00: Video behavioural analysis (1)
Aims: Introduction to the theory and practice of tracking animals in videos, including hands-on training of pose estimation models.
Location: SWC Brasserie Seminar Room
Lead by: Niko Sirmpilatze, Sofía Miñano, Chang Huan Lo
14:00-17:30: Video behavioural analysis
Aims: Using Python to analyse animal tracks produced via pose estimation: cleaning data, quantifying movement, extracting behavioural syllables.
Location: SWC Brasserie Seminar Room
Lead by: Niko Sirmpilatze, Sofía Miñano, Chang Huan Lo
Friday, October 4th
14:00-17:30: Linux and high-performance computing
Aims: To learn some basic principles of high-performance computing (HPC), and run a specific workflow on the SWC HPC system
Location: SWC Ground Floor Lecture Theatre
Lead by: Niko Sirmpilatze, Igor Tatarnikov, Adam Tyson
Monday, October 4th
11:00-12:00: General microscopy: basics
Aims: Learn basic concepts about microscopy to enable specific histology analyses
Location: SWC Brasserie Seminar Room
Lead by: Rob Campbell
13:00-14:30: General microscopy: applications
Aims: Learn basic concepts about microscopy to enable specific histology analyses
Location: SWC Brasserie Seminar Room
Lead by: Rob Campbell
14:30-17:30: Histology analysis (1)
Aims: Introduce napari and the BrainGlobe ecosystem of tools along with some basic image analysis concepts
Location: SWC Brasserie Seminar Room
Lead by: Alessandro Felder, Igor Tatarnikov, Adam Tyson
Tuesday, October 5th
10:00-11:00: Histology analysis (2)
Aims: Learn how to register whole brain microscopy data to an atlas, and analyse structures within the images.
Location: SWC Ground Floor Lecture Theatre
Lead by: Alessandro Felder, Igor Tatarnikov, Adam Tyson
14:00-17:30: Histology analysis (3)
Aims: Learn how to detect cells in large images, and analyse and visualise the results
Location: SWC Ground Floor Lecture Theatre
Lead by: Alessandro Felder, Igor Tatarnikov, Adam Tyson
Full details
software-skills.neuroinformatics.dev/courses/software-skills
Any questions?
software-skills.neuroinformatics.dev | 2024