{"id":10155,"date":"2017-06-14T12:49:32","date_gmt":"2017-06-14T10:49:32","guid":{"rendered":"https:\/\/news.embl.de\/?p=10155"},"modified":"2024-03-25T09:59:16","modified_gmt":"2024-03-25T08:59:16","slug":"1706_image-data-resource","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/1706_image-data-resource\/","title":{"rendered":"Open imaging data for biology"},"content":{"rendered":"\n

A picture may be worth a thousand words, but only if you understand what you are looking at. The life sciences rely increasingly on 2D, 3D and 4D image data, but its staggering heterogeneity and size make it extremely difficult to collate into a central resource, link to other data types and share with the research community.<\/p>\n\n\n\n

To address this challenge, scientists at the University of Dundee, the European Bioinformatics Institute (EMBL-EBI)<\/a>, the University of Bristol and the University of Cambridge have launched a prototype repository for imaging data: the Image Data Resource (IDR)<\/a>. This free resource, described in Nature Methods<\/em>, is the first biological image repository that integrates data from multiple laboratories.<\/p>\n\n\n\n

The IDR also reveals the potential impact of sharing and reusing imaging data for the life sciences.<\/p>\n\n\n\n

Pooling resources<\/h2>\n\n\n\n

\u201cImaging will only be truly transformative for science if we make the data publicly available,\u201d explains Alvis Brazma, a lead author and Senior Scientist at EMBL-EBI. \u201cScientists should be able to query existing data to identify commonalities and patterns. To enable this, we need a platform where researchers can upload imaging data and access data from other experiments. The Image Data Resource is the first step towards creating a public image data repository for the life sciences.\u201d<\/p>\n\n\n\n

There are many resources worldwide in which people publish imaging data, but none of these repositories is both generic and linked to other relevant bio-molecular data. This means that for all the effort that goes into them, it is difficult to reuse these datasets in new studies.<\/p>\n\n\n\n

There are many reasons why sharing imaging data has been so difficult until now \u2013 most notably the heterogeneity and complexity of the image data, but also a critical mass of storage, compute and curation expertise.<\/p>\n\n\n\n

\u201cImaging data is large, yes, but the real challenge is that it is heterogeneous and multidimensional,\u201d says Jason Swedlow, senior author of the study and Professor of Quantitative Cell Biology at the University of Dundee. \u201cCurating, storing and analysing imaging data require significant effort and computing power. The creation of the IDR prototype was only possible thanks to a strong collaboration between several scientific organisations.\u201d<\/p>\n\n\n\n

Nice picture \u2013 but what does it mean?<\/h2>\n\n\n\n

IDR contains a broad range of imaging data, including high-content screening, super-resolution microscopy, time-lapse and digital pathology imaging. But it\u2019s not just the diversity of data types that makes the resource unique; it is the additional information available that creates the added value.<\/p>\n\n\n\n

\u201cIDR doesn\u2019t just show you an image or a video of a cell. It also tells you what the image is about, where it was taken, by whom and what conclusions can be drawn from it,\u201d continues Brazma.<\/p>\n\n\n\n

The new resource integrates imaging data with molecular and phenotype data. For example, IDR includes information on experimental protocols: parameters, analyses and the effects scientists have observed in cells and features. This makes it possible for users to analyse gene networks \u2013 potentially revealing previously unknown interactions \u2013 on a scale that would not be possible for individual studies. That requires a staggering amount of storage and compute power. The IDR collaboration was able to launch their project successfully thanks to the Embassy Cloud resource and support at EMBL-EBI.<\/p>\n\n\n

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The Image Data Resource<\/h2>\n

The prototype public image repository contains a broad range of data, including:<\/p>\n