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Add API to get alternate focal planes in Hamamatsu and other formats #31
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Would Hamamatsu multiplane images help on this or is just an issue of revamping the API? |
It's really about revamping the API. However, it's true that our public dataset doesn't have any multiplane VMS or NDPI slides, and those would be helpful for testing once the API changes have been made. Can you contribute samples? |
We can contribute one NDPI and one MRXS both multi plane images. How should I send it? |
@jetic83 Thanks for the offer! Please hold onto them for now. We're currently reworking our process for accepting slide samples, and I'll get back to you once that's done. |
@jetic83 can you send me "MRXS both multi plane images", we will try to parse them and give some feedback in case of success. |
@bgilbert any news on how to send those two example slides? They can be downloaded here and can be used and changed without restrictions. ndpi_5_layer.zip mrxs_5_layer.zip Would be nice to see the focal planes also in openslide. At the moment, openslide can open these files showing only one layer. |
I had to remove them, since my quota exceeded. How can I share the example slides with you? |
I can give you file storage if needed, if @bgilbert doesn't have some sort of public ftp. |
i can download from anywhere, google drive maybe ?
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I need this feature as well. I have a couple of files that are a few gigabytes that contain a bunch of focal planes, I think I can share them if you want them, but I would have to discuss with some faculty staff first. |
I need this feature as well. I can give a hamamatsu ndpi sample via google drive: hamamatsu_5-layers.ndpi Hamamatsu also provides NDP.viewer software to read it. Just press [Ctrl] and slide your mouse roller to check other layers. |
@tt-leader if you want to automate this kind of task right now you can use https://www.imnc.in2p3.fr/pagesperso/deroulers/software/ndpitools/ (which is what I used). Someone even made a nice python wrapper for the command line parameters: https://github.com/fepegar/ndPytools |
@bergwerf Thanks for your work, it helps me a lot. |
I have some multiplane Aperio SVS files and am willing to contribute attention and effort to get this implemented. I'm not sure if this feature request will or won't resolve this:
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Anyone who can share sample slides with multiple focal planes, please submit them here. |
In DICOM WSI, apparently Z stacks were historically sometimes stored within a single Series, but CP 2135 added an explicit Pyramid UID which requires distinct pyramids to be stored in distinct Series. Our file correlation currently relies on the Series Instance UID, and would need to be broadened to use the Acquisition UID if available. |
_Imported from Trac. This issue originally by _agoode* at 2010-04-26T20:31:48Z.*
Hamamatsu VMS can contain files with distinct focal planes. We need another API to support this. We can avoid reading these other planes for now.
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