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

Wed Dec 7 23:07:27 GMT 2016

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

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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