Graphical Interface¶
Launch the graphical interface by running eubi-gui in the terminal. The four
short videos below walk you through one complete job: converting several images
to OME-Zarr, and then inspecting one of the outputs.
The videos cover the common scenario: one-to-one conversion from a collection of files. More advanced features such as aggregative conversions (concatenation of multiple files), editable batch tables, custom configuration files and editing output metadata are all supported by the interface but not yet demonstrated in the videos; demos for those will be provided soon. In the meantime the CLI reference describes the API, and every control in the interface carries a tooltip.
Linux users
The graphical interface needs Qt's system libraries, which pip does not
install. If eubi-gui stops with libEGL.so.1: cannot open shared object
file, install them with
sudo apt install libegl1 libgl1 libxkbcommon-x11-0 libdbus-1-3 libxcb-cursor0
on Debian or Ubuntu. The eubi command-line interface needs none of them.
1. Selecting input and output folders¶
Navigate to your images, filter them with include and exclude patterns (which
accept star * expressions), tick the files to be converted, and choose where
the OME-Zarr output should be written.
2. Choosing conversion parameters¶
Work through the parameter tabs. The tabs cover different parameter categories ranging from resource allocation, through reader options, chunking, sharding and compression, downscaling, channel and pixel metadata overrides, and more. Each field explains itself on hover, and settings can be saved to a configuration file for reuse.
3. Running a conversion¶
Start the job and watch it progress. The log reports each file as it is read, converted and downscaled, so a failure points at the file that caused it.
4. Inspecting the result¶
Switch to the Inspect tab to open one of the converted OME-Zarr stores from the list in the sidebar. In the Inspect/Metadata path, find full OME-Zarr metadata, including axis names, units, pixel sizes, the chunk and shard layout and compression per pyramid level. Pixel sizes and units can be corrected here and saved back into the OME-Zarr. Switch to the Inspect/Viewer path and visualise the OME-Zarr. Adjust a specific resolution layer via Zoom slider. Browse through the z slices or timepoints. Pan the frame of view using the left mouse button. Add or remove specific channels, and adjust the channel metadata such as colours, viewed pixel range and channel names. The updated visualisation metadata can also be saved back into the OME-Zarr.
The recordings are attached to the v0.1.2-media release. They are not part of the repository, so cloning or pip-installing the package does not download them.