About myHDF5
myHDF5 is an online HDF5 file viewing service developed and maintained by the European Synchrotron Radiation Facility (ESRF) as part of the European PaNOSC project. It is based on H5Web, a React/WebGL viewer for exploring and visualising HDF5 files, as well as h5wasm, a WebAssembly port of the HDF5 C library developed by the NIST that allows reading HDF5 files with JavaScript.
Opening local files
myHDF5 supports opening local HDF5 files of any size, either by selecting them via a file picker from the Open HDF5 page, or by dragging and dropping them anywhere on the interface at any time. You can even select/drop multiple files at once.
Opening remote files
myHDF5 supports opening HDF5 files that are served statically through the web. To do so, simply paste the URL of a file in the field located on the Open HDF5 page. Note that the server must accept cross-origin requests.
A number of hosting services such as Zenodo and GitHub allow downloading raw files. However, it is not always easy to find the right URL to use. To make it easier, myHDF5 accepts the following user-facing URL formats:
- Zenodo download URL (from a record page, right-click on file, Copy Link)
- GitHub permalink (recommended for sharing)
- GitHub URL with tag, branch or commit sha
Note that GitLab currently does not support cross-origin requests. You can still paste a user-facing GitLab URL, but myHDF5 won't be able to fetch the file and will show an error. When this occurs, myHDF5 lets you download the file manually so you can open it as a local file.e.g. https://gitlab.com/utopia-project/utopia/-/blob/master/test/core/cell_manager_test.h5
Sharing a link to myHDF5
When opening a remote file (i.e. a file hosted on Zenodo, GitHub, etc.), the URL of myHDF5 shown in the browser's address bar is shareable as is. This feature does not work for local files.
Supported HDF5 compression plugins
myHDF5 supports reading datasets compressed with any of the plugins available in h5wasm‑plugins@0.0.3.
Known limitations
- External links and virtual datasets in HDF5 files are not supported. While you should see an explicit error for external links, it won't be the case for virtual datasets, which will appear filled with zeros (or with the dataset's fill value, if set).
- Local files are not persisted. If you leave myHDF5 and come back later, or even just reload the page, local files will be removed from the list of opened files.
Where to find support
- For issues/features related to the H5Web viewer, please use H5Web's issue tracker on GitHub
- Otherwise, please use myHDF5's issue tracker on GitLab
- You can also contact us on H5Web's support & feedback mailing list: h5web@esrf.fr
Where to leave feedback
We'd love to hear what you think of myHDF5 and the H5Web viewer! Here are the best ways to get in touch with us:
- Open a discussion thread on H5Web's GitHub repository
- Drop us a line at h5web@esrf.fr