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Add API to get alternate focal planes in Hamamatsu and other formats #31

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agoode opened this issue Sep 16, 2010 · 14 comments
Open

Add API to get alternate focal planes in Hamamatsu and other formats #31

agoode opened this issue Sep 16, 2010 · 14 comments

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@agoode
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@agoode agoode commented Sep 16, 2010

_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.

@andor-pierdelacabeza
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@andor-pierdelacabeza andor-pierdelacabeza commented Feb 3, 2014

Would Hamamatsu multiplane images help on this or is just an issue of revamping the API?

@bgilbert
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@bgilbert bgilbert commented Feb 5, 2014

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?

@jetic83
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@jetic83 jetic83 commented Feb 3, 2017

We can contribute one NDPI and one MRXS both multi plane images. How should I send it?

@bgilbert
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@bgilbert bgilbert commented Feb 13, 2017

@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.

@Lojka59
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@Lojka59 Lojka59 commented Jul 7, 2017

@jetic83 can you send me "MRXS both multi plane images", we will try to parse them and give some feedback in case of success.
We are currently working on same issue.
My e-mail: glojka@gmail.com

@jetic83
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@jetic83 jetic83 commented Oct 3, 2017

@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
Can be viewed e.g. with Aperio's Imagescope.

mrxs_5_layer.zip
Can be viewed e.g. with 3DHistech's Caseviewer.

Would be nice to see the focal planes also in openslide. At the moment, openslide can open these files showing only one layer.

@jetic83
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@jetic83 jetic83 commented Oct 4, 2017

I had to remove them, since my quota exceeded. How can I share the example slides with you?

@andor-pierdelacabeza
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@andor-pierdelacabeza andor-pierdelacabeza commented Oct 4, 2017

I can give you file storage if needed, if @bgilbert doesn't have some sort of public ftp.

@Lojka59
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@Lojka59 Lojka59 commented Oct 4, 2017

@bergwerf
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@bergwerf bergwerf commented Feb 26, 2018

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.

@tt-leader
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@tt-leader tt-leader commented Mar 28, 2018

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.

@bergwerf
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@bergwerf bergwerf commented Mar 28, 2018

@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

@tt-leader
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@tt-leader tt-leader commented Mar 29, 2018

@bergwerf Thanks for your work, it helps me a lot.

@neurophil
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@neurophil neurophil commented Mar 18, 2019

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:
openslide-show-properties multiplane.svs

Openslide-WARNING **: Downsampled images not correctly ordered: 1 < 16.0025
openslide-show-properties: imagesandbox/1323.svs: Not a file that OpenSlide can recognize

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