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

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agoode opened this Issue Sep 16, 2010 · 13 comments

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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.

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andor-pierdelacabeza Feb 3, 2014

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

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

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bgilbert Feb 5, 2014

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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?

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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?

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jetic83 Feb 3, 2017

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

jetic83 commented Feb 3, 2017

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

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@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.

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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.

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Lojka59 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

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

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jetic83 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 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.

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jetic83 Oct 4, 2017

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

jetic83 commented Oct 4, 2017

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

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andor-pierdelacabeza Oct 4, 2017

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

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

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Lojka59 commented Oct 4, 2017

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bergwerf 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.

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.

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tt-leader 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.

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.

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bergwerf 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 did). Someone even made a nice python wrapper for the command line parameters: https://github.com/fepegar/ndPytools

@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 did). Someone even made a nice python wrapper for the command line parameters: https://github.com/fepegar/ndPytools

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tt-leader Mar 29, 2018

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

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

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