New integrations and improved visualisation for imaging data published in GigaDB
GigaDB (http://Gigadb.org) is an open data hosting platform integrated with the open science journal, GigaScience - both of which implement the FAIR (Findable, Accessible, Interoperable and Reusable) principles. It is a curated database with a focus on data and informatics tool reuse. To foster this, our curators engage with GigaScience authors in order to make all the raw and intermediary data, computational tools and data processing pipelines described in the papers available, and where possible, executable on an informatics platform. GigaDB currently hosts over 1,700 datasets from multiple disciplines, such as genomics, proteomics, neuroscience and increasingly more imaging data, such as fMRI and MRI, and 3D X-ray MicroCT images.
Imaging data can be difficult to analyse and peer review for reproducibility, and the ability to better interact with and visualise such large-scale and high resolution images in detail is essential. In order to better support this, GigaDB has recently been integrated with two new tools - SketchFab and ThingiVerse. In addition, we are exploring the use of OMERO as a means of providing web-based zoomable views of whole-slide imaging (WSI) data. Here we will describe the new imaging visualisation and interactive tools integrated with GigaDB, with examples, and show how they improve user experiences, and further support imaging data reuse.
Better visualization of imaging data
3D visualisations are powerful means to explore any specimen in detail. Sketchfab (http://sketchfab.com) is the world’s largest platform to visualise, share and interact with 3D images. Thingiverse - is a platform dedicated to sharing user-created digital design files, and is commonly used by the Maker & DIY Tech communities. GigaDB has embedded both SketchFab images in associated dataset landing pages and are now also able to embed these in an online version of the published paper.
The OMERO zoom viewer allows whole-slide images to be explored at cellular resolution in the context of a web browser, and without need for data download. This example shows a lymph node section from a breast cancer patient and highlights pan-and-zoom functionality, and how to find image resolution. The image resolution is utilised by the scale-bar, which is additionally dependent on the user-specified zoom level. The whole-slide images (WSI) used in this example are available from GigaDB.
Click on poster image to enlarge
GigaScience and its integrated open database, GigaDB aims to revolutionize publishing by promoting reproducibility of analyses and data dissemination, organization, understanding, and use. As an open access and open-data journal and database, we publish ALL research objects (data, software tools and workflows) from 'big data' studies across the entire spectrum of life and biomedical sciences. These resources are managed using the FAIR Principles for scientific data management and stewardship that state that research data should be Findable, Accessible, Interoperable and Reusable.
Our datababase, GigaDB, has had several new integrations with imaging tools that enhances a users ability to interact and better visualise large-scale imaging datasets. Presenting this at the upcoming RDA15 meeting in Melbourne, will be greatly beneficial in terms of sharing ideas, and learning of other new technologies relevant to our open database goals, and open science innovation.