!NEW! TS14 Bordeaux 2020

7th NEUBIAS Training School for Early Career Investigators (TS14), Bordeaux 2020

  • Bordeaux, February 29-March 3 (Sat-Tue), 2020 (conference begins on March 4th!)
  • Number of available seats for trainees:  25
  • Invited trainers: >10
  • Application deadline: December 12th
  • Results from selection: December 20th
  • Confirmation and processing of admin fees by Jan 17th 2020

 Topics:

  • NOTE – This TS14 for Early Career Investigators is opened for both researchers and imaging facility staff, who already have some basic knowledge of dealing with image data, e.g. using the ImageJ user interface, and want to learn how to build and automate image analysis workflows using ImageJ macro scripting. If, however, you are already familiar with image analysis and at least one scripting language, you may be too advanced for this school and should instead consider applying for the TS15 Bioimage Analysts school, which takes place in parallel.
  • Principles of ImageJ Fiji
  • Introduction to workflow automation: record & reuse commands, scripting of workflows/pipelines
  • Building practical workflows to analyse bioimages using macros to extracting and validating quantitative numerical data from bioimages
  • Introduction to ilastik, integration of ilastik segmentation into ImageJ Fiji macro workflows
  • Overview of existing software for bioimage data analysis
  • "WOYOD" - solve your own problem, code your workflow and explore different IA strategies with help from Analysts

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Requirements

  • MUST BE ABLE TO BRING OWN LAPTOP and prepare it in advance!
  • Must have own data to bring to the school which they have started analysing, and be able to explain what they need to learn about image analysis to advance their research (explained in application form).
  • Must already have experience with a toolbox such as ImageJ/FIJI.
  • Must submit valid application form (link at the end of this page) before the deadline (see above) - no exceptions!
  • Must include brief letter of motivation (text pasted into registration form), mentioning level of proficiency and interests, and propose a mini-project with goals for the school (e.g., a specific image analysis workflow or tool - what help is required from our expert trainers?)
  • Must be able to attend all days/times of the course (no exceptions!)
  • Must comply to administrative conditions and confirm travel & hotel by deadline (see above) – read conditions at end of application form!

Trainers (confirmed; more being invited...)

Brief programme  (preliminary)

Coffee-breaks @10:30/16:00, lunches @13:00

Day 1 (Sat)

  • 9:00 Welcome
  • Introduction to image analysis components, workflows, and tools.
  • Image Basics
  • Image segmentation
  • Image measurements, ROIs & Results tables
  • “Natural history of fake data” lecture
Day 2 (Sun)

  • Image convolution and morphological filters
  • ImageJ macro Programming
  • Batch  processing
  • ImageJ ActionBar
  • Webtool : Biii.eu & Biasflow
  • 18:00 TS Gala dinner
Day 3 (Mon)

  • Machine learning based image analysis with ilastik
  • Integrating ilastik into ImageJ macro workflows
  • Special topic (Students' choice)
  • Work on Own Data
Day 4 (Tue)

  • Work on own data, discuss code,present results & wrap up
  • Satellite event
Day5-7

NEUBIAS season finale Symposium
@EINSERB - MATMECA
(all TS participants get a free pass to the NEUBIAS symposium to all events, except Gala dinner)

In addition to this programme, all trainees are invited to attend also the satellite event (Tue), and will get a free pass to the Symposium (Wed-Fri) which includes Call4Help, OSSL- Open-source Software Lounge and other exciting events - full programme here (access to the Symposium gala dinner [Thu] costs 50€)

Fees, conditions and what is, and what is not, included ?

    • Attendance to all days of the course is mandatory for all accepted trainees
    • Trainees need to bring their own laptops to follow the school and exercises.
    • Once accepted we will contact trainees with instructions to install all materials
    • Accepted trainees will be asked to pay administrative fees (350 euros, except if affiliated to ITC* countries: 200 euros)
    • Payment through credit card or bank transfer: all info provided once registered
    • Trainees receiving a travel grant from COST (see below) do not pay any fee
    • All trainees are provided with coffee breaks, lunch and the TS gala dinner
    • All trainees get a free pass to the Symposium and all events (except symposium gala dinner, which costs an additional 50€)
    • Travel & accommodation arrangements are not included for trainees (see below how to travel to venue and hotels nearby):* ITC countries Inclusiveness Target Countries: Albania, Bosnia and Herzegovina, Bulgaria, Cyprus, Czech Republic, Estonia, Croatia, Hungary, Lithuania, Latvia, Luxembourg, Malta, Moldova, Montenegro, Poland, Portugal, Romania, Slovenia, Slovakia, Republic of North Macedonia, Republic of Serbia and Turkey.

Venue & contacts

The event is organised and hosted by Dr. Fabrice CordelièresBordeaux Imaging Center, and Dr. Florian LevetIINS and Bordeaux Imaging Center

For details about the training schools send email to neubias.ts@gmail.com

For local logistics, the local organization team can be reached at any time per email to neubias(dot)bordeaux(at)gmail(dot)com

 

TS programme organizers:

Inquiries should can addressed to: neubias.ts@gmail.com

Venue

 About Bordeaux 

Bordeaux is a port city on the Garonne in the Gironde department in Southwestern France. Awarded for the 5th consecutive times in 2018 as the most attractive town in France, Bordeaux remains a prominent powerhouse and exercises significant influence on the world wine industry. Bordeaux wine has been produced in the region since the 8th century. The historic part of the city is on the UNESCO World Heritage List as "an outstanding urban and architectural ensemble" of the 18th century. After Paris, Bordeaux has the highest number of preserved historical buildings of any city in France.

A leading international research university, the University of Bordeaux promotes the development of training, research and knowledge transfer within its numerous clusters of excellence: neuroscience, medical imaging, environment/climate, advanced materials, archaeology, lasers/optics, digital certification, health and society and cardiology.

Join us for the NEUBIAS conference in Bordeaux and explore the many attractions we have to offer!

Venues

The 4th NEUBIAS conference will be hosted at two sites of the University of Bordeaux. Training Schools + Taggathon (29 February – 03 March 2020) take place at the Centre Broca Nouvelle-Aquitaine in Bordeaux, home of the Interdisciplinary Institute for Neuroscience (IINS) and Bordeaux Imaging Center (BIC). The Symposium (04-06 March 2020) takes place at the ENSEIRB-MATMECA in Talence. Both locations are conveniently located close to the city center of Bordeaux by tram.

Please note that the Satellite Meeting of the Symposium (March 3rd, afternoon) will be held at the Centre Broca Nouvelle-Aquitaine, and not at the Enseirb.

Training Schools & Taggathon, Satellite Meeting, Feb 29-March 3: Centre Broca Nouvelle Aquitaine

Travel & Hotel info:

How to get to France/Bordeaux

The organization has secured possible discounts if you travel with Air France or KLM.

Attractive discounts, up to -15%, on a wide range of public fares on all AIR FRANCE, KLM and their code-shared flights worldwide.

Event: NEUBIAS Conference 2020

ID Code: 35854AF

Travel Valid Period: 22/02/2020 to 13/03/2020

Event location: BORDEAUX

 Please visit the event website or access directly through this link

Proof of attendance-fare eligibility,

At any point of their journey, passengers have to be able to justify the usage of the discounted AIR FRANCE-KLM Global Meetings & Events fares by showing the proof of attendance-fare eligibility document. You will receive this document automatically when you book your tickets on the online booking platform globalmeetings.airfranceklm.com.

Special thanks

Discounts on the hotels and flights bookings have been made possible thanks to the help of Florine Guionnet from “Bordeaux Convention Bureau” (https://congres.bordeaux-tourisme.com/ and http://www.bordeaux-tourisme.com/)

Staying in Bordeaux (suggested hotels)

Hotel booking is left to the participant's initiative. The organization have secured fixed prices with the Accor group. The rooms are not blocked by any of the hotels: they come as a first-come, first-served basis so you should book your hotel after registering to the conference. As of today, this offer is for 3 hotels:

  • Hôtel Mercure Bordeaux Centre: 120 EUR per night
  • Novotel Bordeaux Centre: 120 EUR per night
  • Ibis Budget Bordeaux Centre Meriadeck : 53 EUR per night

Please be sure to specify your participation in the NEUBIAS conference to benefit from the negotiated room rate.

Click on this link (image) to access the details for those hotels:

Note: The Schools and Symposium are not close! There are on two separate tram line (A for IINS/BIC and B for Enseirb Matmeca). Still most of the hotels are in the center, near both tram lines. For instance Ibis Budget hotel centre meriadeck is at 30 minutes from Enseirb and 20 minutes from IINS/BIC. We recommend TS participants taking an hotel at 10 min walk from place Pey Berland, as it is the location where both tram lines cross.

Here is a list of other hotels located in the historic center of Bordeaux city (quartiers des "Grands hommes", "Quinconces", "Hôtel de ville" and "Mériadeck"). All are close to the tramway stops of line A (direction Le Haillan-Rostan / Pin Galant - Stops: Hôpital Pellegrin, Saint-Augustin, François Mitterand) and line B (direction Pessac Centre/Pessac Alouette – Stop: Arts et Métiers):

Hôtel de France **

Hôtel Gambetta **

Hôtel la Porte Dijeaux **

Hôtel des 4 Sœurs **

Hôtel de l'Opéra **

Hôtel Le Chantry **

Citadines Centre Mériadeck Bordeaux ***

Hôtel Ibis style Bordeaux Mériadeck ***

La Maison du Lierre ***

Hôtel Ibis Mériadeck ***

Best Western Bordeaux-Bayonne Etche Ona ***

Adagio Bordeaux Gambetta ****

Mama Shelter

 

The local organizers welcome you to Bordeaux!

Resultado de imagem para Univ Bordeaux images

 

Travel Grants

NEUBIAS will offer competitive Travel Grants to a number of the Trainees applicants affiliated to institutions in COST member countries or Near-Neighbour Countries or approved European RTD Organisations (check definitions in COST Vademecum here). Please check in the application form how to apply for those grants by filling the additional fields enabling to submit a justification. We typically provide less than 1/3 of the grant applications received, so any documented information provided to demonstrate why you need a travel grant is important for us to fully assess your request. The grants are supported by COST (funding body of the NEUBIAS Action). Eligibility and reimbursement modalities will follow the criteria/general COST policies (check the Vademecum here). Granted trainees will be notified ~1week after the final results of the selection. Please be aware that grants can only be executed AFTER the Training School (daily signature on attendance sheets compulsory for grantees). The grants are attributed at a fixed rate (check registration form for more info) to cover for travel and accommodation.

 

Selection Criteria (for all, including granted Trainees):

Trainees will be selected on the basis of their scientific motivations, as described in their motivation letter. Upon selection, NEUBIAS will seek proof of the candidates status as "early career investigator" or "staff" and of being actively working on the project(s) as described in the motivation letter. Gender balance and geographical distribution will be taken into consideration according to COST policies, and only after pre-selection of eligible/suitable candidates and in the case that applicants are too numerous as compared to the number of available seats. Evaluations of the applications is operated by "double anonymous" (no mention to name, institution, country) review by the Training Schools Evaluation Committee of NEUBIAS.

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