Open Microscopy Environment

Hi,

I've got a largish dataset of the above file type (plus png exports) and was curioius regarding support for that format. I see in your docs (below) that the 'texture' data is ignored, which is what I'm after , and that you're interested in getting more datasets
https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/alicona-3d.html

I'm happy to share the data (or examples thereof) with you to see if you can improve support for the format. If interested please let me know.
Best,

Chris

Dear Chris,

Thank you for the offer, we always love more sample data: the variety greatly assists our regression testing. I guess the PNG exports help us to know how the pixel data is supposed to look which is doubly helpful. You can go ahead and upload to http://qa.openmicroscopy.org.uk/qa/upload/ or if the data is too large then let us know and we will arrange FTP credentials for you (unless from OME we can just network-mount a suitable drive?). Also do let us know if we may share the data publicly or if we must keep it confidential.

We are very tight on resources at the moment with plenty already on our plates so we probably won't be able to come up with any near-term fixes, sorry about that. Though, having more sample data available may help others who might open a PR we could review, if they get around to it before we do.

Cheers,
Mark

Hi Mark,

That's great. I don't think there's a problem with sharing the data publicly, but I'll check and get back to you. It'll be next year now.

Best regards,

Chris

Hi again,

I've made the data available publicly and have organised it in what should be self-explanatory dataset structure. The person generating the data usefully also created png versions of the 2D images. In each dataset there are 4 versions for each file prefix:

.al3D - Alicona file
icon.png - thumbnail image
qualitymap.png - (I think) image showing over/under exposure map
texture.png - full size 2D image

Feel free to use these data as and when it works for you.
https://nightshade.openmicroscopy.org/w ... ject-28925
Best,

Chris

Hi Chris,

You'll need to use the URL at https://omero.lifesci.dundee.ac.uk/webc ... ject-28925
where we've configured the webclient UI to be publicly available (as a public user your nightshade link won't work).

I noticed that when browsing thumbnails as a public user, many thumbnails are missing (e.g. on the 2nd Dataset or the 2nd page of the first Dataset).
This is because there are no rendering settings created for the images and the public user cannot create rendering settings since this is a read-only group.

You should log in to nightshade as yourself and browse ALL the thumbnails in each Dataset. Make sure you go through each page (200 thumbnails per page) using the pagination controls below the thumbnails.

Then check that you can see all the thumbnails as a public user at the link above.

Thanks,

Will.

Thanks for spotting this, Will. All done and looking good