Multiple Image Export

I have performed a watershed script on 2300+ TIF images and I need to export them to a new folder for analysis in another application.

The script and workflow command history does not capture “export” as a command to use in a script. What other ways can I automate the export of 2K TIF files?

Could you provide more information on what exactly you need to export? Some examples:
Annotated areas with cell overlays.
Masks of each cell object.
Color coded masks based on class for each object.
Etc.
There are multiple posts both here on the forum, on the GitHub Issues page, and on Pete’s blog that have additional information, though which ones will help most also depend on the version of QuPath you are using.

I am using milestone 6 of QuPath.

I have applied the optical density sum function to all original TIF files (to show brightness/darkness), and now I want to export all those 2,394 images to a local folder in one action.

Maybe I am trying to use ”Annotated areas with cell overlays” with automated export?Not sure, I’m two days into using the application.

If you are using the Viewer and brightness/contrast list, you haven’t applied a function to the images at all. QuPath doesn’t really have much in the way of image adjustment functions, it is just your view of them that changes.


If you want to create a new image, as above, you need to have the visualization you want selected, and then export the image in the File->Export images section. I used Rendered RGB to get the object layer included.

I’m not sure there is a way to do that by script at the moment. I wanted to do something similar a month or two ago and Pete recommended leaving the command list function open so I could go from image to image exporting relatively quickly.

It could be that this has changed in the intervening time, and Pete might jump in with a way to do it, but I’m afraid that’s all I have. OME-TIFF export for whole slide images using color deconvolved channels is another function that would be neat to have, but there just isn’t enough development time for everything, and he only just got funded a week or two ago! More to come.