Open Microscopy Environment

Hello,

Im new to bio-formats library...
I'm trying to open a ZVI file and get physical dimensions of specific ROI. Physicalsizex on metada is 1.0 and physicalsizey is 1.0
PhysicalSizeUnit is 1um. What does it mean? A pixel is equivalent to 1um?

Thanks.

The Pixels attributes are documented at http://www.openmicroscopy.org/Schemas/D ... tml#Pixels so that resource may help you. If supplied at all then PhysicalSizeX should be a number and PhysicalSizeXUnit should be that number's units; same for Y: together they are indeed the physical quantities saying how large the image pixels are so you are correct to use them in interpreting ROIs. 1um is a surprisingly round number so do feel free to upload the image to http://qa.openmicroscopy.org.uk/qa/upload/ if you would like us to take a look.

Cheers,
Mark

mtbc wrote:The Pixels attributes are documented at http://www.openmicroscopy.org/Schemas/D ... tml#Pixels so that resource may help you. If supplied at all then PhysicalSizeX should be a number and PhysicalSizeXUnit should be that number's units; same for Y: together they are indeed the physical quantities saying how large the image pixels are so you are correct to use them in interpreting ROIs. 1um is a surprisingly round number so do feel free to upload the image to http://qa.openmicroscopy.org.uk/qa/upload/ if you would like us to take a look.

Cheers,
Mark

first of all, thank you.

I really like to post the image but i cant for confidential reasons. I can post the metadata info if you think its useful.

Thanks

That's certainly understandable. No, I don't think metadata-only would help us, so to verify that the pixel size is correct you may want to also try looking in vendor-supplied viewing software to see if it says the same thing for your image. Don't hesitate to ask if you have further questions about Bio-Formats' view of the metadata!

Cheers,
Mark