[ome-devel] Prairie View XML changes for upcoming v5.2 Release

Fri Oct 10 20:53:51 BST 2014

Hi Curtis,

We appreciate all your work.  Just as some clarification, the SamplesPerPixel field in our metadata corresponds to the number of samples (off of our acquisition hardware) that were already binned together to form the pixel value.  We do not provide the ability to write out each individual sample in the Tiff data, so it would make sense that the Bio-Formats Prairie TIFF reader would always set the SamplesPerPixel field in the OME metadata to 1, regardless of the value of SamplesPerPixels field in the Prairie metadata.

For example, with our resonant scanner, we often average 3 raw samples together to form 1 pixel value, and only write the single pixel value to Tiff.  We would like our Prairie XML file to still reflect SamplesPerPixel = 3 so users could go back and reference that value.

Thanks again and let me know if I'm just interpreting your email incorrectly.

Regards,
Jimmy

Jimmy Fong
Software Engineer

Bruker Nano Surfaces Division                      Jimmy.Fong at bruker-nano.com<mailto:Jimmy.Fong at bruker-nano.com>
3030 Laura Lane, Suite 140                               www.bruker.com/nano<https://remote.bruker-nano.com/itweb/www.bruker.com/nano>
Middleton, WI 53562-0677
Phone: +1 608-662-0022 x163
________________________________
We are now Bruker!
Same great products.  Same great technology.
Same great people.  New great name.

________________________________
From: ctrueden.wisc at gmail.com [ctrueden.wisc at gmail.com] on behalf of Curtis Rueden [ctrueden at wisc.edu]
Sent: Thursday, October 09, 2014 5:21 PM
To: Wussow, Mike; Fong, Jimmy
Cc: j.r.swedlow at dundee.ac.uk; ome-devel at lists.openmicroscopy.org.uk; Staniszewski, Kevin
Subject: Re: [ome-devel] Prairie View XML changes for upcoming v5.2 Release

Hi Mike, Jimmy, Kevin and everyone,

> We'll test the reader when it's released and keep you posted about
> what we find.

Thanks for getting back to me (via private mail) with your findings regarding the new PrairieView 5.2 file format reader. I am replying to the public thread to keep others in the loop regarding this work.

== Reading the files as a PrairieView dataset ==

It is important to note that if you select the .xml or .env file, the dataset will be detected as "Prairie TIFF" format, whereas if you select one of the .ome.tif files, it will be detected as "OME-TIFF" format. Completely separate reader code is used in each case. The recent changes I made to the PrairieReader [3] only affect the former case.

In short: please select the .xml or .env file if you wish to use the Bio-Formats Prairie TIFF reader, rather than the OME-TIFF reader.

== SamplesPerPixel issue when reading as OME-TIFF ==

Kevin Staniszewski wrote:
> 1. The "SizeC" attribute is incorrect for all but the first frame.
> This acquisition only contained one channel, but every frame after the
> first reports 5 channels. It appears that the number 5 is coming from
> the "SamplesPerPixel" attribute, as in a separate data set, both
> values reported 6 (using a slightly longer dwell time).
>
> 2. The "SamplesPerPixel" attribute is incorrect for only the first
> frame. The correct value for this acquisition is 5, but the first
> frame reports a value of 1. The value of 1 may be coming from the
> number of channels in the acquisition.

Actually, SamplesPerPixel needs to be set to 1 for the dataset you sent. From the OME-XML schema documentation [1]:

    The number of samples the detector takes to form each pixel value.
    [units:none] Note: This is not the same as "Frame Averaging" - see
    Integration in DetectorSettings

SamplesPerPixel is the actual number of recorded sample values per pixel. If you use the "showinf" Bio-Formats command line tool on the dataset, the following warning is shown:

    SamplesPerPixel mismatch: OME=5, TIFF=1

This indicates that the OME-XML indicates SamplesPerPixel=5, but the TIFF file only contains 1 sample value per pixel (as indicated by the IFD's SamplesPerPixel directory entry—which in this case is absent and hence defaults to 1 according to page 39 of the TIFF specification [2]).

All of that said: I think it is indeed a bug in the Bio-Formats OME-TIFF reader that the first series is marked with "SizeC=1" but subsequent ones are "SizeC=5 (effectively 1)". I will investigate if/how we can fix that on our end.

== Failure to extract (X, Y, Z) stage positions ==

Kevin Staniszewski wrote:
> The experiment that generated this data was a T series that took one
> image at all XY locations. If I use the bio-formats importer to look
> at the OME data, it shows up in a way such that each frame looks like
> a different time point, instead of a different XY position.

Yes, there was a bug! Fixed now:

https://github.com/ctrueden/bioformats/commit/ffa5e3071b2083cc0385032b6fdbcf40b3157271

== Spectral datasets ==

Next on my list is to finish adding support for spectral datasets. Will keep everyone posted, and file a PR as soon as it is ready.

Regards,
Curtis

[1] https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2013-06/ome_xsd.html#Channel_SamplesPerPixel

[2] http://partners.adobe.com/public/developer/en/tiff/TIFF6.pdf

[3] https://github.com/openmicroscopy/bioformats/pull/1306

On Fri, Aug 29, 2014 at 2:34 PM, Jimmy Fong <Jimmy.Fong at bruker-nano.com<mailto:Jimmy.Fong at bruker-nano.com>> wrote:
We appreciate all your work, Curtis.  We'll test the reader when it's released and keep you posted about what we find.

Thanks again,
Jimmy

Jimmy Fong
Software Engineer

Bruker Nano Surfaces Division                      Jimmy.Fong at bruker-nano.com<mailto:Jimmy.Fong at bruker-nano.com>
3030 Laura Lane, Suite 140                               www.bruker.com/nano<https://remote.bruker-nano.com/itweb/www.bruker.com/nano>
Middleton, WI 53562-0677
Phone: +1 608-662-0022 x163<tel:%2B1%20608-662-0022%20x163>
________________________________
We are now Bruker!
Same great products.  Same great technology.
Same great people.  New great name.

________________________________
From: Jimmy Fong [fong at wisc.edu<mailto:fong at wisc.edu>]
Sent: Friday, August 29, 2014 2:30 PM
To: Jimmy Fong
Subject: Fwd: Re: [ome-devel] Prairie View XML changes for upcoming v5.2 Release

-------- Original Message --------
Subject:        Re: [ome-devel] Prairie View XML changes for upcoming v5.2 Release
Date:   Fri, 29 Aug 2014 14:22:28 -0500
From:   Curtis Rueden <ctrueden at wisc.edu><mailto:ctrueden at wisc.edu>
To:     Mike Wussow <Mike.Wussow at bruker-nano.com><mailto:Mike.Wussow at bruker-nano.com>
CC:     Jason Swedlow <j.r.swedlow at dundee.ac.uk><mailto:j.r.swedlow at dundee.ac.uk>, OME Development <ome-devel at lists.openmicroscopy.org.uk><mailto:ome-devel at lists.openmicroscopy.org.uk>, Jimmy Fong <fong at wisc.edu><mailto:fong at wisc.edu>

Hi Mike,

> We noticed that the latest release of the Bioformats reader did not
> contain an update for the Prairie View Files.

Thanks for following up. I have updated the Bio-Formats Prairie file format reader to include support for PrairieView version 5.2 datasets. This work will be merged into the Bio-Formats mainline pending review, and can be browsed here:

https://github.com/openmicroscopy/bioformats/pull/1305

Thanks again for sending details about the new format, and for your continued patience.

Best regards,
Curtis

On Mon, Aug 18, 2014 at 7:41 AM, Mike Wussow <Mike.Wussow at bruker-nano.com<mailto:Mike.Wussow at bruker-nano.com>> wrote:
Hi Jason and the OME Development Team,

                We noticed that the latest release of the Bioformats reader did not contain an update for the Prairie View Files.   We are wondering if there is anything we can do to offer further support so that the capabilities are updated for the next release.  Please let me know if we can help in some way.

Best,

Mike

Michael C. Wussow
Director Product Line Management

Bruker Nano Surfaces Division    mike.wussow at bruker-nano.com<mailto:mike.wussow at bruker-nano.com>
3030 Laura Lane, Suite 140           http://www.bruker.com/nano
Middleton, WI 53562-0677
Phone: +1 608-662-0022 x167<tel:%2B1%20608-662-0022%20x167>
Cell: +1 608-381-8252<tel:608-381-8252>
________________________________

From: Jason Swedlow [mailto:j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>]
Sent: Tuesday, June 10, 2014 4:59 AM
To: Mike Wussow
Cc: OME Development
Subject: Re: [ome-devel] Prairie View XML changes for upcoming v5.2 Release

Hi Mike

Thanks for this info.  It's great to have this spec and the example data.  We'll look at this and let you know if we have any questions or issues.

I don't know if we can get this into our upcoming release, as we already have a lot of work scheduled for that.  We'll definitely cc you on the relevant tickets so you can follow our progress.

Thanks again for this contribution.  We welcome all info and sample data from the commercial imaging community.  Thanks to all at Bruker for their support of Bio-Formats.

Cheers,

Jason

Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee
On 9 Jun 2014 15:54, Mike Wussow <Mike.Wussow at bruker-nano.com<mailto:Mike.Wussow at bruker-nano.com>> wrote:
Dear Bio-formats Community,

Prairie View version 5.2 will be released the first week in July 2014.  With this release we have found it necessary to make changes to our XML files.  We realize that these changes will likely break the Bio-formats reader for our files but were necessary changes that should serve our customers well moving forward.  Therefore we are providing information on the changes and example data sets in advance of our release in the hopes that this community can update the Bio-formats reader to accommodate these changes.

A summary of the changes that have occurred to our XML files can be found here: https://www.dropbox.com/s/sf2e634tpuv6ffh/Prairie%20View%20XML%20Evolution.docx as well as in the text below.

Example data sets can be downloaded here: https://www.dropbox.com/sh/rtd73wcu4oboqt4/AABKM1rdhYLWjFVrw-YA5__Sa

Michael C. Wussow
Director Product Line Management

Bruker Nano Surfaces Division    mike.wussow at bruker-nano.com<mailto:mike.wussow at bruker-nano.com>
3030 Laura Lane, Suite 140           http://www.bruker.com/nano
Middleton, WI 53562-0677
Phone: +1 608-662-0022 x167<tel:%2B1%20608-662-0022%20x167>
Cell: +1 608-381-8252<tel:%2B1%20608-381-8252>

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