SVS: handle optional label and macro images

[sbesson]

See https://forum.image.sc/t/correct-way-to-convert-svs-slides-for-omero-import/50942/.

As described in the Digital Slides and Third-Party Data Interchange, a SVS file may contain a label and/or a macro image. In the majority of the samples, these images are typically tagged with the SubFileType 0x1 and 0x9 although this is not part of the document above.

While other translational libraries like openslide and tifffile handle this optional presence, the current version of the SVSReader contains some assumptions that seem to unconditionally expect these ancillary images e.g.

bioformats/components/formats-gpl/src/loci/formats/in/SVSReader.java

Line 331 in 2564538

seriesCount = ((ifds.size() - 2) / uniqueZ.size()) + 2;

https://forum.image.sc/t/correct-way-to-convert-svs-slides-for-omero-import/50942/13 and https://forum.image.sc/t/correct-way-to-convert-svs-slides-for-omero-import/50942/19 describe how to generate a secondary SVS file from public samples illustrating this use case.

From a quick search across our curated QA repository and the OpenSlide public samples, I found no original SVS file without a label or a macro image but it might be useful to look further for additional representative samples.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/correct-way-to-convert-svs-slides-for-omero-import/50942/22

[MITEL-UNIUD]

Yesterday I was browsing through SVSreader.java to find where macro and label were managed, and there are a couple of areas:

• bioformats/components/formats-gpl/src/loci/formats/in/SVSReader.java

  Line 334 in 2564538

  if (seriesCount > 2) {

  (look at the comment in the else branch)

• bioformats/components/formats-gpl/src/loci/formats/in/SVSReader.java

  Line 475 in 2564538

  if (hasFlattenedResolutions() || i > 2) {

  (again, in the else branch there is the case of pyramid levels without macro/label).

Regarding the availability of examples, by default both macro and label are saved. However, looking at the manual, there is a Scanscope system property DoLabelCapture that sets whether the label is captured or not. As soon as I can go to the scanner place, I will try to acquire an example at least without label.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/correct-way-to-convert-svs-slides-for-omero-import/50942/25

[yijian9725]

For public data, label and lacro images are usually hidden to protect privacy.However, label and Macro images are necessary for internal pathological section image management. I hope you can improve the management function of SVS data.

[sbesson]

As mentioned in #4081 (comment), I could not reproduce this issue anymore with Bio-Formats 7.0.0. Looking at the reader itself, I suspect the relevant changes fully relaxing the assumptions in terms of label/macro images were introduced cc1112f and have been released in Bio-Formats 6.8.0.