IDR Paper Out!

[Jason Swedlow-2]

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 Dear All

A quick note on the issue of image data sharing and publication, which has
been discussed previously in this forum.
We’ve just published a paper describing the Image Data Resource project
(IDR; http://idr.openmicroscopy.org/), a collaborative project between the
Dundee OME team, Alvis Brazma’s group at EMBL-EBI and Rafael Carazo-Salas’
group at Bristol. The paper is published in Nature Methods (
http://www.nature.com/nmeth/journal/v14/n8/abs/nmeth.4326.html) and we have
deposited the author pre-print for open access in PubMedCentral at
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536224/>
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536224/. An editorial that
discusses some of the implications was published by Nature Methods at
http://www.nature.com/nmeth/journal/v14/n8/full/nmeth.4389.html.
In the IDR project, we want to promote the re-use of the image data and
metadata we have received from the study authors. We of course provide a
browseable UI that exposes the metadata integration and curation (getting
all this to work and perform was no small feat!). However, we have also
made the backend database available for download, the full IDR application
deployable by Ansible, and, with support from EMBL-EBI, the image data
downloadable by Aspera. This should allow the community to access IDR data
and technology in many different ways. Community members can build their
own IDRs and integrate their own data and analytic tools. We don’t believe
there will be a single IDR, but rather hope to promote the routine
development and use of integrated imaging resources in projects and
institutions worldwide.
Our work raises several questions. Here are some we have heard, and our
current answers, which might change as things evolve:

   1. Which images should be included in the IDR?  Should a lab submit all
   the image data it has ever collected?  Clearly, we don’t publish our lab
   notebooks and there is little justification for publishing all recorded
   bioscience and biomedical imaging data. The IDR implements the concept of a
   “reference image”, which was defined in a white paper
   <http://www.eurobioimaging.eu/content-news/euro-bioimaging-elixir-image-data-strategy>
published
   by Euro-BioImaging <http://eurobioimaging.eu/> and Elixir
   <https://www.elixir-europe.org/>. The IDR project’s submissions page
   <http://idr.openmicroscopy.org/about/submission.html> details our
   implementation of this concept. There’s no doubt the reference image
   concept will evolve, but this seems to be a useful strategy to get going.
   If you have ideas about definition(s) of “reference image” we'd  love to
   hear from you. (By the way, if you are an ML person, “reference image”
   equates to “images with great labels”.)


   1. What about a standardised data submission template?  We’d love to
   standardise experimental, imaging, and analytic metadata, but that’s not
   yet practical. We have built a metadata template inspired by the ISA-TAB
   formats that we are using for IDR data submissions, and this has proven
   useful for several of our recent datasets. Comments, suggestions and
   updates are always welcome. (Note to imaging system vendors: supporting
   open file formats would help us A LOT!!!!)


   1. How much data can we store and host?  EMBL-EBI is providing hosting
   resources for IDR through their Embassy cloud resource, so they’ll have to
   answer that one.  So far, they just keeping giving us more…


   1. How sustainable is IDR? We think a key part of this issue is
   demonstrating the scientific value of building and maintaining image
   data  resources— that’s where IDR’s focus will be for the next year or so.
   We are certainly working hard to secure long-term funding for IDR resource
   and technology development. We’re very grateful to the BBSRC and Horizon
   2020 for funding work on the IDR to this point.

   If you think IDR is important, please do contact the BBSRC, Wellcome
   Trust, NIH and others and tell them what you think!!!  If you have used the
   images or metadata in IDR, let us know-- examples and results will help our
   case.


   1. Is the IDR a production resource? We’re proud of what we’ve achieved
   with the IDR, and look forward to continuing to grow the number and expand
   the range of datasets it holds. We have a lot more technical development to
   do, and we have only begun to explore the possibilities for analysing and
   integrating IDR data. IDR should therefore not be considered a full
   production resource, but is still a proof of concept or prototype.
   Nonetheless, we expect the images that IDR holds to be available long
   term-- that’s why we have placed IDR at EMBL-EBI. It’s early days and we’ll
   have to see how this field and technology evolves.


   1. How will you federate multiple IDRs? Good question. We applied for
   funding for the infrastructure to do this work twice— the reviews were
   great, but the panels decided not to fund the work. The feedback indicated
   that the panels want us to solve the sustainability problem without grant
   funding. How we were supposed to do this wasn't specified.

As always, we welcome suggestions, comments, feedback, criticism and most
definitely usage and development of these tools. If you are interested in
submitting data to the IDR, see
http://idr.openmicroscopy.org/about/submission.html.
Cheers,
Jason


--
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Centre for Gene Regulation & Expression
School of Life Sciences
University of Dundee
Dundee  DD1 5EH
United Kingdom

phone [phone]
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Lab Page: http://www.lifesci.dundee.ac.uk/people/jason-swedlow
Open Microscopy Environment: http://openmicroscopy.org
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[Julia Fernandez-Rodriguez]

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Dear Colleagues, please feel free to pass this on to anybody that may be interested

The National Centre for Cellular Imaging (CCI) at the University of Gothenburg, is one of the leading academic imaging facilities in Sweden providing expertise and access to advanced microscopy to the research community, both locally and at other Swedish universities and abroad.

The CCI offers high-end microscopy techniques for researchers in the various fields of life science, but also chemistry, physics, material science. The equipment includes several laser scanning (confocal and multiphoton) microscopes, a large number of other fluorescent microscopes, laser microdissection microscope, super-resolution microscopes, as well as a scanning and a transmission electron microscope. The scientific staff at the CCI assists researchers in the experimental designing and planning of microscopy experiments and provides the in-depth training for the operation of the microscopes and for specific imaging techniques. Additionally, support is provided in the processing, rendering and analysis of the acquired datasets.

The CCI is now looking for an experienced Scientific Officer in advanced light microscopy.The purpose of this post is to facilitate the development of novel imaging and analysis methods in close collaboration with PI’s to apply these methods to their specific research questions. The position does not include own research.Job description

Job description

The successful candidate will work in the Centre for Cellular Imaging advanced microscopy facility: 1) Supporting the CCI staff in maintaining different state-of-the-art advanced microscopes; 2) educating and supporting our users, by assisting and training them in sample preparation and instrument use; 3) giving advice on the design of imaging experiments in order to optimize output and research activities; 4) giving support in image processing and analysis, by educating users in the fundamentals of imaging processing as well as the usage of most common image processing/analysis packages; 5) developing new imaging methods required to solve specific problems that may arise in the various research projects; 7) The post holder will also participate in the organization and teaching of practices/lectures for graduate and undergraduate courses.

Qualifications and Experience

We are seeking an ambitious and service-oriented team player with excellent interpersonal and organizational skills. The suitable candidate should hold a MSc/PhD degree in Science (Physics/Biology/Chemistry) or engineering, with at least five years of research and practical experience in advanced light microscopy (confocal, multiphoton, super‐resolution). Skills in high-level programing, handling of large data sets, data evaluation and analysis would be an advantage. A basic knowledge in current biological and biomedical research is essential. Prior experience of working in a microscopy facility is a plus. The candidate should be willing to expand his/her knowledge in new microscopy techniques and be ready to work in a highly interdisciplinary environment. Ability to work under pressure and in a team, with good communication in English and organisational skills is essential. We are looking for an enthusiastic person with a research background who combines technical expertise with strong communication skills, who has a strong will to aid other researcher in their work, but also the motivation to work independently.

Application deadline 21 August 2017

LINK to the application website:

http://www.gu.se/english/about_the_university/job-opportunities/vacancies-details/?id=1027
*****************************************
Julia Fernández-Rodríguez, PhD
Head of the Centre for Cellular Imaging Core Facility
Sahlgrenska Academy, University of Gothenburg, Sweden

Visiting address: Medicinaregatan 7A, Gothenburg
Postal address: Box 435, 405 30, Gothenburg
Delivery address: Medicinaregatan 1G , 413 90 Gothenburg

Telephones: [phone]
                    [phone]
E-mail: [hidden email]<mailto:[hidden email]>
Web: http://www.cf.gu.se/english/Centre_for_Cellular_Imaging/

Swedish National Microscopy Infrastructure - NMI
Web: http://nmisweden.se/

Network of European Bioimage Analysts - NEUBIAS
STSM coordinator  - COST Action CA15124
Web: www.neubias.org<http://eubias.org/NEUBIAS/>