Merging annotations

Congratulations! You have successfully annotated your segmentation. Recall that since the annotated JSON EMDB-SFF does not have any geometry present, you will need to ‘merge’ it together with one that has geometry. This is done using the sfftk CLI.

Before you perform the merge, you may be interested in changing the segment colours. You can do this on the JSON file prior to merging (point 6 in Annotating your segmentation)

First, download the annotated segmentation from SAT. To merge the annotated JSON geometry-less EMDB-SFF annotated.json with the HDF5 geometry-full EMDB-SFF geometry.hff use the following command:

sff notes merge --source annotated.json geometry.hff --output annotated-segmentation.hff --verbose

In the above command, we create a new file (annotated-segmentation.hff) to leave geometry.hff unchanged.