Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

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

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

agoode opened this issue Sep 16, 2010 · 16 comments
Labels
api Requires API changes dimensionality Requires additional image dimensions enhancement format-aperio Aperio SVS format-leica Leica SCN format-mirax 3DHISTECH MRXS format-ndpi Hamamatsu NDPI format-sakura Sakura SVSLIDE format-ventana Ventana BIF format-vms Hamamatsu VMS

Comments

@agoode
Copy link
Member

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
Copy link

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

@bgilbert
Copy link
Member

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?

@bgilbert bgilbert added format-vms Hamamatsu VMS format-ndpi Hamamatsu NDPI format-mirax 3DHISTECH MRXS format-leica Leica SCN labels Dec 15, 2014
@bgilbert bgilbert added the dimensionality Requires additional image dimensions label Feb 11, 2015
@bgilbert bgilbert added format-ventana Ventana BIF format-sakura Sakura SVSLIDE labels Apr 20, 2015
@bgilbert bgilbert added the format-aperio Aperio SVS label Dec 7, 2015
@jetic83
Copy link

jetic83 commented Feb 3, 2017

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

@bgilbert
Copy link
Member

@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
Copy link

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
Copy link

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
Copy link

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
Copy link

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

@Lojka59
Copy link

Lojka59 commented Oct 4, 2017 via email

@bergwerf
Copy link

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.

@VisionTheta
Copy link

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
Copy link

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

@VisionTheta
Copy link

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

@neurophil
Copy link

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

@bgilbert
Copy link
Member

Anyone who can share sample slides with multiple focal planes, please submit them here.

@bgilbert
Copy link
Member

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
api Requires API changes dimensionality Requires additional image dimensions enhancement format-aperio Aperio SVS format-leica Leica SCN format-mirax 3DHISTECH MRXS format-ndpi Hamamatsu NDPI format-sakura Sakura SVSLIDE format-ventana Ventana BIF format-vms Hamamatsu VMS
Development

No branches or pull requests

8 participants