[ome-users] Olympus SlideScan.ini format reader?

Thu Dec 8 17:27:40 GMT 2016

Hi Paul,

> On 7 Dec 2016, at 23:07, Paul Richards <paulrichards321 at gmail.com> wrote:
>
> Hello,
>
> I am just about ready to commit, but have a question. Are multiple magnifications levels stored as different images? Or is that what is referred to by the "z-stack”?

The Z-stack refers to multi-dimensional images where the XY dimensions are preserved but planes are acquired along the Z dimension
i.e. 3D images. Images with multiple magnification levels or pyramidal images are read using the subresolution API of Bio-Formats.

> Currently I have setup as one "submission" but with four different core metadata objects for four magnifications levels. Is this the way?

Creating different core metadata objects is definitely the first step. In order to annotate these images as magnification levels of the same
pyramidal images, you want to:
- order your core metadata objects from the highest resolution (largest XY dimensions) to the lowest resolution (smallest XY dimensions)
- set the resolutionCount field in the first core metadata to be equal to the number of
 subresolutions i.e. something like

 core.get(0).resolutionCount = 4;

Other examples can be found in pyramidal format readers like Imaris HDF [1] or SVS [2].

> I am a bit new to open microscopy, but with other microscopy software you can jump between different magnification levels with the mouse scroll wheel or with a right click popup menu. How do you usually jump between magnifications levels in the OMERO web client?

The behavior is certainly the way OMERO clients handle multi-resolution images - see for instance this histopathology image on the public
IDR server [3]

Hope this helps,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/blob/v5.2.4/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java
[2] https://github.com/openmicroscopy/bioformats/blob/v5.2.4/components/formats-gpl/src/loci/formats/in/SVSReader.java
[3] http://idr-demo.openmicroscopy.org/webclient/img_detail/1920123/

>
> Thanks,
>
> Paul Richards
>
>
> On Tue, Oct 18, 2016 at 10:44 PM, Melissa Linkert <melissa at glencoesoftware.com> wrote:
> Hi Paul,
>
> Thank you very much for your interest in OME.
>
> > I have started two open source programs to view some Olympus SlideScan.ini
> > files and convert into Tiff format. However I cannot get the top level of
> > the pyramid lined up with the second level and was wondering if anyone here
> > could help. Basically there is no Mac or Linux open source viewer for this
> > file format that I know of. If you guys have one please let me know!
>
> No, unfortunately Bio-Formats does not support this format, nor do we
> currently have any relevant example datasets.
>
> > The slides are composed of a ton of jpgs that are tiled and four files with
> > an .ini extention. Each of the four ini files detail a scan magnification
> > level (40x, 20x, 1.25x,etc.) and give the details of the coordinates of the
> > jpgs. Inside the start of the ini files are some initial scanning values, do
> > you know what lXOffset and lYOffset might mean when the slide is scanned? I
> > understand the x and y stage ref variables, image width and height, and step
> > sizes, but not sure what the lXOffset and lYOffset mean. Notice there is
> > [Da0] in my text below which is the first file Da0.jpg. There are a ton of
> > Da?.jpg files and the coordinates are in this file. I understand the x, y,
> > and z coordinates, and the t variable equals time but what also could the s
> > variable mean?
> >
> >
> >
> > The problem I am having is that the levels of the pyramid aren’t aligned
> > right when you zoom in. In other words when I use my own program that
> > renders this or a Leica Windows ImageScope application to zoom in it zooms
> > in on a completely different section of the slide so I know my image data is
> > wrong in my own generated file. I am thinking that the lXOffset and lYOffset
> > might have something to do with it but I tried subtracting or adding these
> > offsets to the start of the next pyramid level but it still doesn’t line up
> > correctly, and overall it doesn’t have much effect actually. I tried
> > performing all kinds of calculations and triple and quadruple checking my
> > own calculations with these offset values for literally *HOURS* and have not
> > had any luck so I am not sure what they mean. The bottom two layers line up
> > ok, but the top layer seems to have been scanned at a different location and
> > can’t figure out how to calculate the starting x and y. It’s not just this
> > slide either, all the slides I use are like this.
> >
> >
> >
> > Any help is greatly appreciated! I know I’m probably short on details, let
> > me know if there is anything else you need to know. I have not published my
> > code anywhere yet, let me know if that would help as well. Basically I am
> > just looking for the method to match the 3rd level up with the 2nd level. I
> > can get my own program to line up one individual slide by adjusting some
> > variables, however it then does not work for the next slide so I know I am
> > missing some part of the equation.
>
> If you are interested in turning your existing code into a new
> Bio-Formats reader, and can supply an appropriate dataset for testing,
> then we would certainly be happy to help in debugging this problem.
> Without seeing example data or code that can be integrated into
> Bio-Formats, however, the OME team unfortunately does not have the
> resources to investigate support for this new format at this time.
>
> For more information on creating a new Bio-Formats reader, please see:
>
> http://www.openmicroscopy.org/site/support/bio-formats5.2/developers/reader-guide.html
>
> and for an overview of our policy on new format development (and why
> we encourage existing code to be contributed as a Bio-Formats reader),
> please see:
>
> http://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/
>
> Regards,
> -Melissa
>
> On Mon, Oct 17, 2016 at 1:02 PM, Paul Richards
> <paulrichards321 at gmail.com> wrote:
> > I have started two open source programs to view some Olympus SlideScan.ini
> > files and convert into Tiff format. However I cannot get the top level of
> > the pyramid lined up with the second level and was wondering if anyone here
> > could help. Basically there is no Mac or Linux open source viewer for this
> > file format that I know of. If you guys have one please let me know!
> >
> >
> >
> > The slides are composed of a ton of jpgs that are tiled and four files with
> > an .ini extention. Each of the four ini files detail a scan magnification
> > level (40x, 20x, 1.25x,etc.) and give the details of the coordinates of the
> > jpgs. Inside the start of the ini files are some initial scanning values, do
> > you know what lXOffset and lYOffset might mean when the slide is scanned? I
> > understand the x and y stage ref variables, image width and height, and step
> > sizes, but not sure what the lXOffset and lYOffset mean. Notice there is
> > [Da0] in my text below which is the first file Da0.jpg. There are a ton of
> > Da?.jpg files and the coordinates are in this file. I understand the x, y,
> > and z coordinates, and the t variable equals time but what also could the s
> > variable mean?
> >
> >
> >
> > The problem I am having is that the levels of the pyramid aren’t aligned
> > right when you zoom in. In other words when I use my own program that
> > renders this or a Leica Windows ImageScope application to zoom in it zooms
> > in on a completely different section of the slide so I know my image data is
> > wrong in my own generated file. I am thinking that the lXOffset and lYOffset
> > might have something to do with it but I tried subtracting or adding these
> > offsets to the start of the next pyramid level but it still doesn’t line up
> > correctly, and overall it doesn’t have much effect actually. I tried
> > performing all kinds of calculations and triple and quadruple checking my
> > own calculations with these offset values for literally *HOURS* and have not
> > had any luck so I am not sure what they mean. The bottom two layers line up
> > ok, but the top layer seems to have been scanned at a different location and
> > can’t figure out how to calculate the starting x and y. It’s not just this
> > slide either, all the slides I use are like this.
> >
> >
> >
> > Any help is greatly appreciated! I know I’m probably short on details, let
> > me know if there is anything else you need to know. I have not published my
> > code anywhere yet, let me know if that would help as well. Basically I am
> > just looking for the method to match the 3rd level up with the 2nd level. I
> > can get my own program to line up one individual slide by adjusting some
> > variables, however it then does not work for the next slide so I know I am
> > missing some part of the equation.
> >
> >
> >
> > Here is the start of FinalScan.ini, a slide magnified at 40x (but there are
> > three other levels to it as well, 20x, and what I think is 1.25x and a
> > “thumbnail” type image at the top of the pyramid):
> >
> >
> >
> > lXStageRef=278000
> >
> > lYStageRef=142500
> >
> > iImageWidth=752
> >
> > iImageHeight=480
> >
> > lXStepSize=1588
> >
> > lYStepSize=1182
> >
> > lXOffset=-554
> >
> > lYOffset=-3444
> >
> > dMagnification=40
> >
> > tImageType=.jpg
> >
> > iFinalImageQuality=70
> >
> > tFolder=Duke Pathology 200
> >
> > lAnalysisImageCount=13421
> >
> > lCalibrationImageCount=0
> >
> > tWebSlideTitle=Kidney, Infarct, Recent
> >
> > tCopyright=
> >
> > tAnimalSource=
> >
> > tBodySystem=
> >
> > tOrganSource=
> >
> > tSlideSource=
> >
> > tPathology=
> >
> > tDescription=
> >
> > tWebSlideCollection=
> >
> > tContributor=
> >
> > tTissueType=
> >
> > tStudy=
> >
> > [Da0]
> >
> > x=125041
> >
> > y=56260
> >
> > z=-15500
> >
> > t=7
> >
> > s=2
> >
> > [more tile coordinates clipped, from Da1 to Da13420…]
> >
> >
> >
> > Paul F. Richards
> >
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
>
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