NEW! TS7 Szeged, Feb 2018

Training School TS7 for Analysts

  • Jan 27-30th (Sat-Tue) – the Symposium will start on Jan 30th, immediately after the Training Schools; all TS7 participants are invited to attend for free (requires separate registration!)
  • Number of available seats for trainees:  35
  • Registration deadline: Nov 9th!
  • Selection Results: Nov 11th
  • Confirmation & payment before Dec 14th. 

Aim:

The school aims at providing bioimage analysts with practical access to the latest bioimage analysis workflows and their components. Many software/library packages are updated and new ones are appearing on a daily basis, but analysts tend to be constrained to what one knows already and omit the use of new components. They are too busy. We hope that this school will become a good chance for analysts to be exposed to the latest scene in the bioimage analysis, of various workflows and workflow components, to widen their scope and broaden their skills.

The school program is largely renovated from last year, based on the feedback of participants. The webpage of the school last year is available here. Evaluation and feedback can be found here (PDF).

 

Organizers

  • Jean-Yves Tinevez, BioImage Analyst, Pasteur Institute – Paris, France
  • Kota Miura – Image Analyst @University of Heidelberg, Germany & NIBB, Okazaki Japan

The Program

The school will be organized in four types of modules:

  • Workflow Deconstruction
  • Algorithms of Workflow Components
  • Forums
  • Implementation.

In Workflow Deconstruction, we reproduce, trace and modify bioimage analysis workflows. Invited speakers and selected workflow authors from participants present their bioimage analysis workflow in details: the biological problem, algorithms of components including statistical analysis, how they are assembled into the workflow to output either numbers, plots or visualization results. In parallel with these explanations, participants will load those components and reproduce the workflow in their own laptop (reproduce the workflow). Interactive discussion on each of the components, the overall design of the workflow and capability of running the workflow in various environments are moderated.

In Algorithms of Workflow Components, invited speakers present an in-depth explanation about workflow component. These talks are aimed at encouraging participants to expand their knowledge towards the utilization of more efficient, more precise algorithms in their workflow. Following discussions are planned to be moderated.

  1. Discussion and comparison with similar components (plugins, a function in a library, etc) implemented for a similar purpose.
  2. Discussion on interoperability. How to use those components in various ecosystems e.g. Java, Python, MATLAB, R.

In Forums, we will discuss various aspects related to bioimage analysis – with interests surrounding analyst as a profession (e.g. How do we teach bioimage analysis?). Discussion results are summarized and will be reported to the NEUBIAS community.

In Implementation, participants are split into several groups and each group implements one of the following assignments:

  1. Modification of workflows presented in the school, for either:
    1. the full workflow running in different ecosystems
    2. a part of the workflow replaced with a different component.
  2. Comparison and benchmarking of workflow components with similar algorithms. The target components should be selected by each group.

Requirements

  • Participants are expected to be bioimage analysts, analyzing biological image data on a daily basis.
  • Participants are expected to be fluent in at least one programming language. We do not teach coding, but intensively do coding using several different languages. Skills/flexibility to follow such sessions are a prerequisite.
  • Participants must bring and be ready to use their own laptop.
  • There will be no helpers during all sessions. Participants are asked to help each other.
  • During registration, the applicant is asked to submit at least one bioimage analysis workflow that one has authored/worked on (starting with a specific biological question, describe the workflow in a short paragraph and the type of results: numbers, plots and/or visualization – does not have to be a published paper). Among these applicants, some are selected for presentation as “Workflow Deconstruction” session and lead the session – a detailed planning of the session together with organizers will be asked to the selected people prior to the school.
  • Must be able to attend all days & times (no exceptions!)
  • Must guarantee payment of administrative fees well in advance of school dates and by Bank transfer only!
  • Must comply with administrative conditions and confirm travel&hotel at least 1 month in advance– read conditions at end of application form!

Workflow Deconstruction: Details

  • Tracing the workflow, starting with sample image data, understand the biological problem, do image processing and data analysis, ends up in numbers, plots or visualizations.
  • The explanation for each step (or each component) are given and interesting algorithms are picked up and discussed in details.
  • Each participant uses ones own laptop to reproduce/modify the workflow
  • Interactions: questions on components, the proposal for alternative solutions, discussion on capability in other ecosystems.
  • Invited “workflow authors” + Selected “workflow authors” from applicants (registration form should include an abstract of submission of interesting workflow)

Invited Workflow Authors / Workflow Component Speakers (more to be announced)

  • Assaf Zaritsky (Workflow Author)
    • Image analysis for decoupling global bias and local interactions.
    • https://elifesciences.org/articles/22323
  • Molnár Csaba (Workflow Author, High Content Screening, and Analysis)
  • Vasja Urbancic (Workflow Author, Analysis of Filopodia)
    • Image analysis of filopodia, and their statistical treatments
    • http://jcb.rupress.org/content/early/2017/07/28/jcb.201705113
  • Fabrice Cordelières (Speaker, Workflow Component)
  • Tobias Pietzsch (Speaker, Workflow Component)
  • Anna Kreshuk (Speaker, Workflow Component)

Schedule (preliminary)


What is, and what is not included for trainees?

  • All selected participants are provided with catering (coffee break, lunch and dinner, excluding breakfast) and course materials in electronic format.
  • Participants will have a free pass to the Symposium that follows after the schools, and have free access to all sessions and events.
  • Room will be equipped with Ethernet connection for all participants laptops, but each will be responsible for providing power, ethernet and vga adaptors.
  • Travel & accommodation are not included for trainees
  • There is a limited number of travel grants available (see below!).

Venue & contacts

TS6 will take place at the Institute of informatics of the University of Szeged.

  

The University of Szeged, Institute of Informatics

The Institute of Informatics was established in 1990 as part of the Faculty of Science and Informatics at the University of Szeged. Its main task is to teach modern computer science and information technology and to take part in innovative and research-and-development projects. The Institute offers BSc, MSc and teacher training programs and also provides basic education of informatics at several other programs of the Faculty of Science and Informatics at the University of Szeged.

Students have the chance to travel, work or do research abroad, to study one or two semesters at foreign universities, and are also welcome to join the research projects going on at the Institute.

MSc graduates interested in research can join one of the many exciting research projects of our PhD School of Informatics, established in 2002.

Besides performing educational tasks, the Institute implements research-and-development and innovative projects with institutional and industrial partners.

The Institute publishes an English language journal, Acta Cybernetica (https://www.inf.u-szeged.hu/kutatas/acta-cybernetica), which is an important forum and output of research activity and PhD training.

https://www.inf.u-szeged.hu/en

Hotels & Local Transport

For participants of TS6 rooms have been pre-booked in Hotels Tisza and Art (more information on the Symposium page). Both hotels are reasonably priced and close to the venue. When students learn about the selection results (Nov 15th), they should contact the hotel of choice directly, mention code “NEUBIAS2018” and confirm reservation dates and billing information (check page above for details about payment process and deadlines).

Hotel Tisza and Hotel Art are both within walking distance (10 minutes and 4 minutes) from the Training Schools’ venue. From Hotel Tisza you can also take the tram (line 1 or 2) for 2 stops to the TS venue (from Széchenyi tér to Aradi vértanúk tere).

 

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 checkthe application form how to apply for those grants by filling the additional fields enabling to submit a justification. 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 November 16th, and grants will be executed ONLY after the Training School (daily signature on attendance sheets compulsory for grant winners). The grants are attributed at a fixed rate of 650€ to cover for travel and accommodation expenses.

 Selection Criteria (for all, including granted Trainees):

Trainees will be selected strictly on the basis of their scientific motivations, as described in their motivation letter. Upon selection, NEUBIAS will seek proof of the candidates status as “Analysts”. 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.

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