Publishing from whole-slide scan images


This is a very naive post. With the development and growing use of whole-slide scanner, a lot more biologists, including myself, would sometimes not go to a “standard” microscope but rather directly scan the whole slides, in particular to perform some kind of quantification, in QuPath for example. The questions becomes what happens for publication… would journal generally accept snapshots taken from the software? Or would they require cropped tiff images? What is your exeprience of such situation?

Many thanks

I have generally seen snapshots with “appropriate” levels of manipulation being submitted, with the understanding that the original is available if necessary to back up that image data was treated in a reasonable manner. Many journals will have something like this:

Those tend to cover the format required for the images that will go in figures. Keep the originals, be ready to submit them if needed. Hosting the whole slide images somewhere is probably “good for science” though not everyone has the means (or rights, when it comes to patient data) to do this.

In fact, using the QuPath citation page, you can see what other authors, including Pete in his original paper, have done.

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Hi @rmvl,
What I usally do is a figure with original/computed crop to show how detections look like.
I also use very often a full resolution image with an insert to show the whole slide image. This allows to locate your crop in the whole architecture of the tissue and tho show details of interest.