Workflow file for EMPIAR Upload

Hi all,

Is there a way to generate a workflow file similar to Scipion (workflow.json) that can be uploaded to EMPIAR along with the RAW files so anyone can reproduce the results in CryoSPARC?

Thank you


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I want to bump this thread now that workflows are released with 4.4. Is the JSON file from exporting a cryosparc workflow compatible with EMPIAR’s workflow visualization?

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Hi @prash & @sbliven ,

CryoSPARC workflows can be exported as .json files and are able to be imported into any instance. More information on this feature can be found in the guide: Workflows - CryoSPARC Guide.

In regards to the workflow visualization feature in EMPIAR, we have noted this feature for investigation and will look into the possibility of supporting it in the future.

- Kelly

Everything is JSON nowdays. :wink: The trick is using a standard data model that can interoperate with other software. Is the data model documented anywhere?

EMPIAR’s data model is also not well documented (I would have expected it here). I suspect that they only support Scipion workflow files.

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Thanks @sbliven - at the moment we don’t have the schema documented but we’ll definitely consider publishing it in the near future. Do you happen to know of an EMPIAR entry that includes a Scipion workflow?

- Suhail

The Scipion3 paper cites three: EMPIAR-10891, EMPIAR-10516, and EMPIAR-10514. The EMPIAR website seems to be down though so I can’t verify.

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