I’m attempting to input custom metadata categories for files through my processing pipeline, e.g. the date and version of X macro used, the specific input fields, and some simple outputs I’d like to keep track of through my pipeline. The setMetadata(“Info”, string) and Property.setList(string) functions seem like a decent solution, especially since I’m able to call them easily using Property.get().
So I ran into an issue using Bio-Formats. TLDR, seems like Bio-Formats hasn’t integrated these Property Functions since they came out with 1.53a. Basically:
- Custom metadata & properties set using either setMetadata(“Info”, string) or Property.setList(string) are not saved if using Bio-Formats exporter. Must use saveAs(“Tiff”, title) instead.
- Custom metadata & properties saved using the above saveAs(“Tiff”, title) method are overwritten if opened with Bio-Formats. The properties read “No properties” and the metadata is just canned image properties like dimensions, etc.
Big picture gripe: In general, ImageJ/FIJI tends to like to drop metadata during processing. It would be great if the default was to carry the metadata forward so that images have a paper trail. It’s a bit annoying having to consciously pull the metadata from the source file and write it to the processed one, especially if that process itself ca become onerous and non-intuitive for large amounts of metadata. Carrying over an image’s dimensions properties, like pixel/voxel size and frame interval, would be really helpful for bookkeeping. Maybe it already does this, but if it does, I have no idea how to retrieve these data…
Bonus bug: I noticed that when saving an image as an .ome.tif, if there is already a file present at that path, rather than overwriting it, Bio-Formats just expands to the file size, as if it is concatenating the images. This would be cool if, like an HDF5 file, you can have subdirectories/imagesubsets within an ome.tif, but as far as I can tell this isn’t the case (e.g. the seriesCount and imageCount are unchanged, despite the increased file size).