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

[Paul Richards]

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
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