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ImagingDataCommons / slim

Interoperable web-based slide microscopy viewer and annotation tool
https://imagingdatacommons.github.io/slim/
Apache License 2.0
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Support for multiple focal planes (z stacking) #123

Open DrexlerChao opened 2 years ago

DrexlerChao commented 2 years ago

Hi Sir,

Z-stacking involves scanning a glass slide at different focal planes along the vertical z-axis and stacking the images on top of each other to produce a composite multiplane image. Z-stacks can be merged to create a detailed 3 dimensional representation of the sample.

Some WSI scanners that offer z-stacking capability. For example, 3DHistech, Hamamatsu, Leica, etc.

We are not sure if Slim or DICOM microscopy viewer JavaScript library supports Z-stacks display? If yes, it will be easily used after feeding DICOM into viewer. If not, any information we need to know from DICOM or scanner manufacturer?

Any help would be sincerely appreciated. Thanks.

hackermd commented 2 years ago

Thank you for creating the issue @DrexlerChao.

The Slim application and the underlying dicom-microscopy-viewer library (see https://github.com/herrmannlab/dicom-microscopy-viewer/issues/80) do currently not support interactive visualization of images with multiple focal planes (z-stacks).

I just tested it in Slim with a 3DHistech image. It resulted in an error message "Images with multiple focal planes are not yet supported." Unfortunately, the error is only printed into the console, but is not reported to the user via the user interface (same issue as #122).

It would not be difficult to extend the viewer to support navigation of z-stacks (switching between different focal planes) but it has not been a priority for us so far and would require some development work.

In the short term, we will improve error handling so that the user knows why the viewer does not display the image. In the mid to long term, we can think about adding support for multiple focal planes.

DrexlerChao commented 2 years ago

Hi @hackermd,

Thanks for your clearly explanation. We are looking forward the Slim application and the dicom-microscopy-viewer library support z-stacks image in the future.

With sincere appreciation.