Brainhack Western France

Open science hackathon

November 14-15, 2019

An event of BrainHack Global


Keynote speakers

Reversible Networks for Brain MRI Synthesis
François Rousseau, November 14, 13:30

Title to be confirmed
Anne-Charlotte Philippe, November 14, 14:00

Expert Aided CNNs: improving fracture classification with curriculum learning
Diana Mateus, November 15, 13:30

Title to be confirmed
Nancy Bertin, November 15, 14:00


Registration (before November 5)


Submit a Project!

What?


Brainhack events convenes engineers, researchers and clinicians to work together on projects related to neuroscience. Are you are interested in sciences and neurosciences? Come and learn about existing tools or bring your own projects and find passionate people to join.


There is a lot of open data available (e.g. 101 nights, FC 1000, OASIS, etc.), waiting to be analysed ! Are you looking for contributors on an existing software? Would you like to meet new collaborators? Do you have open questions in your research? Come and discuss with us during these 2 days.
Brainhack Rennes will feature presentations from key researchers in our community as well as video links to the global community. Visit BrainHack Global 2019 to learn more about events worldwide.

Who?


  • Camille Maumet (Program committee)
  • Emmanuel Caruyer (Program committee)
  • Julie Coloigner (Program committee)
  • Raphaël Truffet (Program committee)
  • Édith Blin (Local Organising Committee)
  • Armelle Mozziconacci (Local Organising Committee)

Where?


The conference will be held in Rennes, at INRIA Rennes-Bretagne-Atlantique / IRISA, on the university campus (called “Campus de Beaulieu”), in the east of Rennes.

To reach Inria from the city center, you can

  • walk (about 30 minutes),
  • take a bus (more information: Star – public transportation service – only in French) or
  • rent a bike (more information: Velo Star).

This map explains how to reach INRIA from the bus Station “Tournebride” : Map from bus stop

If you need informations about accomodations, please contact us !

More information here.

IRISA/Inria Rennes
Campus de Beaulieu
35000 Rennes, France

Share ideas

Build Projects

Meet the community

Learn Tools

Keynote speakers

Reversible Networks for Brain MRI Synthesis
François Rousseau, IMT Atlantique, Brest.

Image synthesis in medical imaging is an emerging research area and the main applications are data normalization, cross modality synthesis, super-resolution, validation of algorithms (segmentation, registration). In this talk, we will tackle the problem of image synthesis as a regression problem, formulated in a deep learning framework. More specifically, we will explore the use of deep reversible networks for brain MRI synthesis.

Title to be confirmed
Anne-Charlotte Philippe, Université Bretagne Sud, Vannes.

Expert Aided CNNs: improving fracture classification with curriculum learning
Diana Mateus, Ecole Centrale Nantes.

We target the problem of fracture classification from clinical X-Ray images towards the development of an effective Computer Aided Diagnosis (CAD) system. The fracture classification problem is difficult as confirmed by low intra- and inter-expert agreement rates of our in-house study and also in the previous literature. The talk will show the design and application of different deep learning techniques towards identifying, localizing and finally classifying proximal femur fractures. In particular, a recently proposed curriculum learning approach which takes expert knowledge into account to guide the CNN weight optimization.

Title to be confirmed
Nancy Bertin, Univ Rennes, Inria, CNRS, IRISA UMR 6074, Rennes.


Schedule


Current projects


Develop interfaces and workflows for Anima in Nipype

Nipype and Anima

Nipype looks like a great framework to define small processing bricks and automatically assemble them to form pipelines. At last year brainhack, we had time to define interfaces for the Anima open-source software. The idea this time is to go all the way to define a pipeline based on Anima interfaces and try to run it on a cluster on some toy data.

Contact: Olivier Commowick

BULLE (cereBral vascULar bifurcation LabElling)

Intracranial aneurysm

Context and issues ⮟

ICAN is a french multi-center study aimed at bridging clinical observations, genomic markers as well as quantitative imaging biomarkers to better understand the formation, the development and the possible rupture of intracranial aneurysms. Saccular aneurysms are generally localized at vessel bifurcations and several studies have identified the anatomical localization of saccular aneurysms as an important risk factor for rupture. One of the outcomes of ICAN is a large imaging biobank resulting from routine medical imaging exams (ToF MRIs, CTs, or DSAs) provided by the 34 french participating academic hospitals. This data can be accessed for further analysis through the Shanoir database. However the analysis of the geometrical features of the bifurcation that carry the IA is hampered by the lack of anatomical labelling. Determining to which artery belongs a bifurcation carrying a saccular aneurysms is a time-consuming task and requires expertise in brain anatomy.

Objectives and expected outcomes

BULLE aims to design and implement an atlas-based neuroimaging processing workflow for automatic labelling of the cerebrovascular trunk, also known as the circle of Willis. These approaches, known as atlas-based segmentation, are based on the registration between an anatomical atlas and the patient images, and the subsequent transfer of annotations from the atlas to the images. We expect to gather experts in 3D MRI registration and vascular imaging. Based on their expertise we will collaboratively develop a reusable Jupyter notebook dedicated to the automatic annotation of cerebral vessels.

Contact: Olivier Commowick

Your project!

Is there a topic you are particularly interested in? A tool you would like to work on? Submit your own project!

Projects can cover any type of software development, but also can be a proposal for a focus discussion or, a self-training using public resources, and even more! All project proposals will be considered, please contact us if you are unsure whether your proposal can be submitted as a project. To submit a project, please email us a project title and a short description with an image.


Further Information

Brainhack Western France 2019. This 2-day workshop will be held November 14-15th at IRISA / Inria, Rennes, France, and is part of BrainHack Global 2019, where a constellation of such events happen simultaneously around the globe. Brainhack events convenes researchers from a myriad of disciplines to work together on projects related to neuroscience. Similar to hackathons in the tech sector, much of the schedule is left open for attendees to work together on projects of their choosing. We also include “unconference” sessions where talks are chosen by the attendees based on their interests as they evolve throughout the meeting. Brainhacks are not “coding sprints” or exclusive to programmers, but rather are open to brain scientists from all backgrounds.

Hacking: The core of Brainhack are “open hacking” sessions during which attendees collaborate together on projects of their choosing. Attendees who have specific project ideas or data that they would like to explore are encouraged to submit their project below prior to the event. At the opening of the Brainhack event, typically after the ice breaker, attendees pitch their ideas and afterwards mingle with others to organize a project team. Teams work together throughout the remainder of Brainhack and are given the opportunity to present their progress during the wrap-up session at the end of the event.

“Hackathons are based on collaboration, not competition”

Unconference: Sessions for attendees to present their research or other topics of current interest. Immediately prior to these sessions, the agenda is determined on-site. Attendees who are willing to present add their name to a sign-up sheet.

Working papers on the outcomes from Brainhack Western France can appear in the Gigascience Brainhack Thematic Series, and shorter project reports from the event are eligible for the annual Brainhack Proceedings.

Thanks to generous support from Inria, registration is free, and includes 2 lunches and all coffee breaks. Registration will be open shortly.

Brainhack Western France is generously supported by:

Inria IRISA

Brainhack Western France is hosted by:

Inria IRISA

Get In Touch!


Contact us for information or with your ideas.

Join us on Slack #bhg19-rennes

Code of Conduct

Brainhack is dedicated to providing a harassment-free conference experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion. We do not tolerate harassment of conference participants in any form. Sexual language and imagery is not appropriate for any conference venue, including talks. Conference participants violating these rules may be sanctioned or expelled from the conference without a refund at the discretion of the conference organizers.

Harassment includes, but is not limited to:

  • Verbal comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion.
  • Sexual images in public spaces
  • Deliberate intimidation, stalking, or following
  • Harassing photography or recording
  • Sustained disruption of talks or other events
  • Inappropriate physical contact
  • Unwelcome sexual attention
  • Advocating for, or encouraging, any of the above behaviour


Enforcement

Participants asked to stop any harassing behavior are expected to comply immediately.

Organizers and presenters are also subject to the anti-harassment policy. In particular, they should not use sexualized images, activities, or other material.

If a participant engages in harassing behaviour, event organisers retain the right to take any actions to keep the event a welcoming environment for all participants. This includes warning the offender, expulsion from the conference with no refund or not being allowed to participate in future events.

Event organisers may take action to redress anything designed to, or with the clear impact of, disrupting the event or making the environment hostile for any participants.

We expect participants to follow these rules at all event venues and event-related social activities. We think people should follow these rules outside event activities too!


Reporting

If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible. You can report to Camille or Julie. Harassment and other code of conduct violations reduce the value of our event for everyone. We want you to be happy at our event. People like you make our event a better place.

You can make a report either with your personal email or using an anonymous email.


Past Editions