NEUBIAS Pasteur course on Bioimage Analysis

Paris, Institut Pasteur, from Tuesday the 30th of May to Friday June the 2nd.
In-person only.
Training school focused on Bioimage Analysis.
Two parallel tracks:
- Early career investigators track: Learn to master the tools and techniques of bioimage analysis for your own research. From power usage to building analysis pipelines.
- Analysts track: Learn to use and deploy advanced tools; learn to master high-performance computing for advanced bioimage analysis.
Number of available seats: 20 students max for each track.
Selection based on project description.
Bonus session on Friday afternoon: Work on your own data, with the help of colleagues and experts.
Timeline:
- Registration deadline: 28th of April
- Notification of acceptance: 8th of May
Course fee: 300€ VAT included. Fee includes the course, catering on Tuesday, Wednesday and Thursday. Fees can only be paid by wire transfer with a purchase order.

Topics.

Both tracks of the course have a specific focus on hands-on and interactive tutorials. They are meant to be convivial and foster a collaborative atmosphere between students and teachers.

Early-career investigator track.

In this course you will learn how to use the most recent and common image analysis software tools. You will learn to master and use them for your own research project. The course will walk you from their installation, basic usage to building image analysis pipelines, from raw images to quantification results.

In the beginning we will explore the usage of software such as Fiji, Icy, QuPath, Napari, Ilastik, TrackMate… By the end of the course you will able to use and edit scripts and notebooks for batch processing and some advanced analysis.

You should apply to this course if you are a biologist and / or have no or little background in image analysis and do imaging in your research project. No knowledge of coding is required.

A small part of this course is covered in the PhD program of Pasteur (in case you attended it), but it is small and required so that everyone has the same bases.

Analyst track.

The strong focus of this course is the use of advanced algorithms and computing resources for bioimage analysis. Its aim is to equip analysts with the skills to use high-performance computing resources and GPU acceleration, that are becoming ubiquitous among research infrastructures. We will also learn how to use and deploy advanced tools for tracking, denoising, and image-processing in general.

The main tools of this track will be Python, Napari and Fiji.

Some minimal experience with scripting and python usage is required.

Requirements.

Bring your own laptop to install the tools we’ll be working with and to access the HPC resources of Pasteur.

Also, absolutely bring a mouse with the laptop :) It’s painful to use the tools mentioned above with the trackpad.

Participants are encouraged to bring image data for the ‘Work on your own data’ sessions.

Program.

Teachers.

Joanna PYLVÄNÄINEN – Turku BioImaging, Finland.
Anne-Sophie MACÉ – Institut Curie, Paris France.
Joran DESCHAMPS – Human Technopole, Milan Italy.
Ko SUGAWARA – RIKEN, Japan.
Robert HAASE, Till KORTEN – Physics of Life, Dresden Germany.
Véronique LEGRAND, Konstantin PETROV, High-Performance Computing core facility, Institut Pasteur, Paris France.
Marvin ALBERT, Gaëlle LETORT, Minh-Son PHAN, Stéphane RIGAUD, Jean-Yves TINEVEZ, Image Analysis Hub, Institut Pasteur, Paris France.

Timetable.

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Be aware: this is still a preliminary schedules, modification can still occur.

On Friday afternoon, after the course, there will be a bonus ‘Work on your own data’ session, during which all students and teachers are welcome. This time will be used to review the course concepts and apply these on image data contributed possibly by you.