As discussed in our previous post, we have now extended our NGFF specification to support high-content screening.
The OME team is leading a community effort to design a new cloud-friendly “Next Generation” file format (NGFF). See the announcement and other image.sc posts tagged with ome-ngff.
This blog is an update about the use of C++11 and C++14 (“modern C++”) within OME Files C++.
The challenges and cost associated with the development and maintenance of software for reading images stored in proprietary file formats (PFFs) have been discussed at length in previous blog posts 1, 2. One approach to help address these issues is the development of community collaborations that provide sustainable solutions to PFF support in Bio-Formats.
This is an update about what we are working on in the Bio-Formats codebase for the next few months. As this is where the OME Data Model lives, it covers our current and upcoming work on the Model and the Bio-Formats project.
You may have noticed that a few months ago, we received an email asking us about when we expect to support 3D HISTECH .mrxs files. This sort of request isn’t particularly unusual and the reply gives an insight into one of the key challenges we face.
Current development on Bio-Formats can be grouped into four categories:
In our first two posts we looked at the principles of building standards in a rapidly innovating field like modern biological and biomedical imaging. We also reviewed the technical concepts we have used to build the OME Data Model and Bio-Formats, to explain OME’s efforts to deliver a common library for accessing scientific image data. In this next entry, we describe how we work with the community to build Bio-Formats.
This blog is an update about what we are working on in the OME Files and Bio-Formats codebase for the next few months.
For several months the OME team has been working on what will soon be released as the new 2016 OME Data Model. The OME Data Model specifies Regions of Interest (ROIs) in terms of a set of Shapes. As OMERO 5.3 will use the new Data Model, the upcoming changes include an initial round of adjustments that improve consistency between Shape representations in the Data Model and OMERO. They will each also include a significant addition: Folders, a new top-level model object.
This is an update about what we are working on in the Bio-Formats codebase for the next few months. As this is where the OME Data Model lives, it covers our current and upcoming work on the Model and the Bio-Formats project.
Current development on Bio-Formats can be grouped into four categories:
As discussed in our previous post, we have now extended our NGFF specification to support high-content screening.
The OME team is leading a community effort to design a new cloud-friendly “Next Generation” file format (NGFF). See the announcement and other image.sc posts tagged with ome-ngff.
After the intensive development period of IDR’s first releases, the 5.4 series of OMERO was intended to be a stable platform for the community and the OME team to build on. From its first release in October 2017 to its tenth and final release this year, 5.4 has, we think, served as a reference point for the community.
Nature Research journal Scientific Data is a peer-reviewed, open-access journal for descriptions of scientifically valuable datasets, and research that advances the sharing and reuse of scientific data. These data descriptors provide a path for publishing datasets associated with scientific publications.
Recently there have been several publications and substantial discussion about the FAIR principles (see for example, Wilkinson et al, 2016 and the Force11 Fair Data Principles). Overall, the goal of the FAIR principles is “to facilitate knowledge discovery by assisting humans and machines in their discovery of, access to, integration and analysis of …scientific data and their associated algorithms and workflows.”1 These principles are extremely powerful but as has been repeatedly noted, the routine implementation of FAIR principles is a significant challenge.
Imaging datasets present a particular challenge for implementing FAIR. The datasets are large, multidimensional and complex. Perhaps most importantly it is probably unrealistic to suggest that a single metadata standard will handle the huge diversity of imaging experiments and datasets. In the best possible case, it is likely that there will be families of metadata standards or flexible APIs, each tuned and designed for accessing specific types of imaging metadata.
OME has been working on the image data publication problem for many years. Our recent work on the Image Data Resource (IDR) is an example of an added value database that integrates imaging data from many biological imaging datasets and links gene and drug perturbations with cell phenotypes2. IDR focuses on reference image datasets, i.e. those datasets that have high levels of biological and molecular annotations and have a strong likelihood of re-use by the scientific community.
Our work on IDR has been well-received and the resource is growing in size and usage. However, IDR doesn’t address more routine data publication; the datasets that are not reference images, but are associated with a scientific publication in the biological sciences. For example, our lab in Dundee has recently published a paper that explores the interaction of a single protein Bod1 and the Ndc80 complex, a protein complex that mediates the attachment of microtubules to connect to chromosomes during cell division3. How to publish the imaging data associated with this paper?
As you might guess, we’ve used OMERO to publish and link these data. We’ve used our institutional OMERO server, and used an institutional DOI as the definitive link to the data. The datasets associated with this paper were imported into OMERO as part of the analysis workflows and then were moved into a public OMERO group for publication. The data can be browsed, searched, viewed and downloaded. We believe we’ve made the datasets “AIR”—Accessible, Interoperable and Reusable. Making these datasets truly “Findable” will take more time as we develop routine landing pages and JSON-LD-based metadata for these images.
In the meantime, we thought it might be useful for the community to see how we have achieved this work. With the latest releases of OMERO (5.4 and beyond), we have made it fairly easy for images to be managed and published online. Documentation describing exactly what we did is available4.
We hope this work is an important contribution to the movement for making data available online. We believe we’ve made reasonable progress in making data AIR and look forward to fully achieving the goals of the FAIR principles.
2016 has been a busy year for OME. Many of you will have noticed the number of Bio-Formats releases and the fact that OME Files C++ is now available for implementing the OME Data Model and OME-TIFF support in C++ software (you can read our preprint here).
The challenges and cost associated with the development and maintenance of software for reading images stored in proprietary file formats (PFFs) have been discussed at length in previous blog posts 1, 2. One approach to help address these issues is the development of community collaborations that provide sustainable solutions to PFF support in Bio-Formats.
This is the first of what will hopefully be a series of posts about tools developed by members of the community. Ian Munro of Imperial writes:
The recent EU referendum will undoubtedly have implications for the future of UK science. It now seems equally clear that those implications will remain unknown for some time to come. No matter what happens next, we want to emphasize our ongoing commitment to the OME project and to our community.
For those of you who couldn’t make it to Dundee for OME 2016, or maybe just didn’t get to all the sessions you wanted to, we have a range of content on our downloads site–notes, slides and even movie versions of workshop presentations–available to browse from downloads.openmicroscopy.org/presentations/2016/Users-Meeting/ or linked via the programme page if there is specific content you’re interested in.
You may have noticed that a few months ago, we received an email asking us about when we expect to support 3D HISTECH .mrxs files. This sort of request isn’t particularly unusual and the reply gives an insight into one of the key challenges we face.
This is a quick update on the status of various versions of OMERO, and some discussion about our future development plans and aspirations.
We are in the process of getting rid of submodules and separating our code into smaller repositories. Why? And why should developers and users care?
In our first two posts we looked at the principles of building standards in a rapidly innovating field like modern biological and biomedical imaging. We also reviewed the technical concepts we have used to build the OME Data Model and Bio-Formats, to explain OME’s efforts to deliver a common library for accessing scientific image data. In this next entry, we describe how we work with the community to build Bio-Formats.
After the intensive development period of IDR’s first releases, the 5.4 series of OMERO was intended to be a stable platform for the community and the OME team to build on. From its first release in October 2017 to its tenth and final release this year, 5.4 has, we think, served as a reference point for the community.
2016 has been a busy year for OME. Many of you will have noticed the number of Bio-Formats releases and the fact that OME Files C++ is now available for implementing the OME Data Model and OME-TIFF support in C++ software (you can read our preprint here).
This blog is an update about what we are working on in the OME Files and Bio-Formats codebase for the next few months.
The recent EU referendum will undoubtedly have implications for the future of UK science. It now seems equally clear that those implications will remain unknown for some time to come. No matter what happens next, we want to emphasize our ongoing commitment to the OME project and to our community.
For several months the OME team has been working on what will soon be released as the new 2016 OME Data Model. The OME Data Model specifies Regions of Interest (ROIs) in terms of a set of Shapes. As OMERO 5.3 will use the new Data Model, the upcoming changes include an initial round of adjustments that improve consistency between Shape representations in the Data Model and OMERO. They will each also include a significant addition: Folders, a new top-level model object.
The OME team has always been committed to building specifications and software that are cross-platform solutions and that support as many different types of users as possible, including those with limited IT support/budget. In keeping with our open source ethos and the fact we rely on public and charity grant funding, we also try to use open source tools as part of our workflows for testing, building and deploying our products wherever possible. We do support commercial operating systems and platforms — we build and test OMERO.insight on Windows, actively work to support accessing the OMERO and Bio-Formats APIs in Matlab, and actively support browsing OMERO.web using IE.
This is an update about what we are working on in the Bio-Formats codebase for the next few months. As this is where the OME Data Model lives, it covers our current and upcoming work on the Model and the Bio-Formats project.
This is a quick update on the status of various versions of OMERO, and some discussion about our future development plans and aspirations.
Following our published roadmap for Java support we are ending support for Java 6 with the release of OMERO and Bio-Formats 5.2 later this year.
For the past few years, we have supported the distribution of the OMERO Java desktop clients as Java Web Start Applications. This feature was requested by several institutions and we are aware that some continue to use it. We acknowledge that Java Web Start is a practical and still active way to distribute the applications. But, due to the steady increase of issues not under our control, continuing to support the use of Java Web Start for distribution of the OMERO Desktop clients is not sustainable and is likely to become impossible in the near future.
We are in the process of getting rid of submodules and separating our code into smaller repositories. Why? And why should developers and users care?
Current development on Bio-Formats can be grouped into four categories:
The OME team has always been committed to building specifications and software that are cross-platform solutions and that support as many different types of users as possible, including those with limited IT support/budget. In keeping with our open source ethos and the fact we rely on public and charity grant funding, we also try to use open source tools as part of our workflows for testing, building and deploying our products wherever possible. We do support commercial operating systems and platforms — we build and test OMERO.insight on Windows, actively work to support accessing the OMERO and Bio-Formats APIs in Matlab, and actively support browsing OMERO.web using IE.
Following our published roadmap for Java support we are ending support for Java 6 with the release of OMERO and Bio-Formats 5.2 later this year.
For the past few years, we have supported the distribution of the OMERO Java desktop clients as Java Web Start Applications. This feature was requested by several institutions and we are aware that some continue to use it. We acknowledge that Java Web Start is a practical and still active way to distribute the applications. But, due to the steady increase of issues not under our control, continuing to support the use of Java Web Start for distribution of the OMERO Desktop clients is not sustainable and is likely to become impossible in the near future.
A user reported last week that after a Java upgrade, it was no longer possible to connect to the OMERO server using OMERO.insight. Since then we’ve been looking into the issue. A fix is ready as well as a few steps for the future.
The OME team has always been committed to building specifications and software that are cross-platform solutions and that support as many different types of users as possible, including those with limited IT support/budget. In keeping with our open source ethos and the fact we rely on public and charity grant funding, we also try to use open source tools as part of our workflows for testing, building and deploying our products wherever possible. We do support commercial operating systems and platforms — we build and test OMERO.insight on Windows, actively work to support accessing the OMERO and Bio-Formats APIs in Matlab, and actively support browsing OMERO.web using IE.
This is a repost from the figure.openmicroscopy.org blog where its creator Will Moore talks about how OMERO.figure works:
This is the first of what will hopefully be a series of posts about tools developed by members of the community. Ian Munro of Imperial writes:
This blog is an update about the use of C++11 and C++14 (“modern C++”) within OME Files C++.