[ome-users] MetaMorph tif scaling

[David Gault (Staff)]

Hi Dotan,

Thank you for providing the sample data set for testing. I was able to test the dataset provided with the latest Bio-Formats release (5.7.2) and when opening either the .nd file or the .tif (while the .nd is present) the PhysicalSize X and Y are showing as 0.645 microns and the X and Calibration match. Without the accompanying .nd file I see a value of 32.05 microns.

What value of PhysicalSizeX and PhysicalSizeY were you reading when opening the .nd file via the Bio-Formats Importer?
Also which operating system are you using and which version of Bio-Formats and FIJI have you installed?
(Versions can be found in FIJI under Help > About ImageJ and Help > About Plugins > Bio-Formats Plugins )


With Thanks,
David Gault

On 27 Dec 2017, at 14:48, Dotan Kamber <Dotan.Kamber at eb1.co.il<mailto:Dotan.Kamber at eb1.co.il>> wrote:

Dears,

I'm facing an issue with scaling of MetaMorph tif images acquired with VisiView when opening with FIJI.
When separate tif images are saved as part of an "experiment " with accompanying .nd file the images are opened  with the correct scaling (nm/pixel) using the Bio-Formats importer when pointing to the tif images but not upon pointing to the .nd file or upon drag-and-drop to FIJI.
The scaling is also wrong when a single image (without accompanying .nd file) is opened both via drag-and-drop and the Bio-Formats Importer.
the same images are opened by Drag and Drop.
The following files have been uploaded –
Experiment_2_GFP.nd
Experiment_2_GFP_t1.tif
Experiment_2_GFP_t2.tif
Experiment_3_GFP.tif
For all the correct scaling is 0.645 microns per pixel
This value shows up in the parameters XCalibration and YCalibartion.
It seem that the wrong scaling is retrieved from the parameters XResolution and Yresoltion

Happy new year!
Dotan

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