General software skills for systems neuroscience#

Overview#

Held over seven days, this course will provide researchers with some basic computational skills for systems neuroscience research. This will include general programming, software development best practices and data analysis using leading open-source software tools. This course will also include some general microscopy lectures.

Schedule#

Date	Time	Event	Location
Monday, September 30th	13:00-17:30	Introduction to Python (1)	SWC Brasserie Seminar Room
Tuesday, October 1st	09:45-10:45	Data management and sharing (1)	SWC Ground Floor Lecture Theatre
	15:00-17:30	Data management and sharing (2)	SWC Ground Floor Lecture Theatre
Wednesday, October 2nd	10:00-12:30	Introduction to Python (2)	GCNU Seminar Room
	13:30-17:30	Version control and software development best practices	GCNU Seminar Room
Thursday, October 3rd	10:00-13:00	Video-based analysis of animal behaviour (1)	SWC Brasserie Seminar Room
	14:00-17:30	Video-based analysis of animal behaviour (2)	SWC Brasserie Seminar Room
Friday, October 4th	14:00-17:30	Linux and high-performance computing	SWC Ground Floor Lecture Theatre
Monday, October 7th	11:00-12:00	General microscopy: basics	SWC Brasserie Seminar Room
	13:00-14:30	General microscopy: applications	SWC Brasserie Seminar Room
	14:30-18:00	Histology analysis (1)	SWC Brasserie Seminar Room
Tuesday, October 8th	10:00-11:00	Histology analysis (2)	SWC Ground Floor Lecture Theatre
	14:00-17:30	Histology analysis (3)	SWC Brasserie Seminar Room

Introduction to Python#

The aim of the course is to introduce basic concepts of programming in Python, and establish a community of Python users. It is a hands-on course, in which we will guide you through the process of writing your first Python script and teach you some best practices.

The course will run over two days, 2.5-3h per day with a break in between.

Full details can be found on the course webpage

Instructors: Igor Tatarnikov, Sofía Miñano

Version control and software development best practices#

The aims of the course are

to learn how to keep track of changes to your code with Git and GitHub,
to learn how to structure your code well
and to get an initial idea of how work collaboratively on a code base, and how to document and test your code.

Git and Github slides for 2023/2024 course

Site for software development best practice

Instructors: Stephen Lenzi, Laura Porta, Alessandro Felder

Video-based analysis of animal behaviour#

This course will introduce the theory and practice of tracking animals in videos to quantify their behaviour. Participants will get to train pose estimation models with SLEAP, analyse pose tracks with movement, and extract behavioural syllables with keypoint-moseq.

Important

Please install the necessary software and download the required data ahead of the course. Full details can be found on the course webpage. If you encounter any issues, please contact Niko Sirmpilatze.

Instructors: Niko Sirmpilatze, Chang Huan Lo, Sofía Miñano

Linux and high-performance computing#

This course will introduce some basic principles of using Linux, and high-performance computing in general. Most of the course will be centered around learning to run a specific workflow (pose estimation) on the SWC HPC system.

Full details can be found on the course webpage.

Instructors: Niko Sirmpilatze, Igor Tatarnikov, Adam Tyson

General microscopy#

This course will introduce some basic concepts about microscopy (optics, fluroescence etc.) to help better understand the following course on histology analysis.

Instructors: Rob Campbell, Adam Tyson, Alessandro Felder, Igor Tatarnikov

Histology analysis#