Export result is empty

[Dadatata-JZ]

Hi Andy,

Thanks for sharing this. I copied your script to QuPath Script Editor, but got empty list in my exported json file. I don't have much experience with QuPath. I assume these annotations on the left should be included in object annotationMeasurements but they are not.

Please kindly give me some suggestions. Thank you in advance.

[choosehappy]

take a look at the associated blog post: http://www.andrewjanowczyk.com/exporting-and-re-importing-annotations-from-qupath-for-usage-in-machine-learning/ in particular the section called: "QuPath Type"

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On Fri, Jul 23, 2021 at 6:21 PM Pre-Dr.Jz ***@***.***> wrote: Hi Andy, Thanks for sharing this. I copied your script to QuPath Script Editor, but got empty list in my exported json file. I don't have much experience with QuPath. I assume these annotations on the left should be included in object annotationMeasurements but they are not. Please kindly give me some suggestions. Thank you in advance. [image: Screen Shot 2021-07-23 at 12 19 41 PM] <https://user-images.githubusercontent.com/31292151/126811842-dbedecfb-9fac-4b11-b7df-fb9f336788b2.png> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACJ3XTD3KYTEWNK3SUKD4DDTZGJIBANCNFSM5A4JRG5A> .

[Dadatata-JZ]

Sorry for missing such handy notes! Thanks

[Dadatata-JZ]

Hi Andy,

An additional question, do you by any chance know how to export a batch of annotations files? I have a list of whole slide images with annotations and want to export them in jsons for deep learning labelling. However, opening them in QuPath GUI manually is quite time-consuming.

Thanks

[choosehappy]

if you create a project and put all your files into it, you will be able to click run for project:

this will run the code once per file

if you're interested in taking a pure python approach, you can check out paquo: https://github.com/bayer-science-for-a-better-life/paquo