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Physical size = 1.0

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
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Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Physical size = 1.0

Postby borja » Tue Jan 17, 2017 1:36 pm

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.
borja
 
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Joined: Tue Jan 17, 2017 10:53 am

Re: Physical size = 1.0

Postby mtbc » Wed Jan 18, 2017 9:52 am

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
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mtbc
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Re: Physical size = 1.0

Postby borja » Wed Jan 18, 2017 10:44 am

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
borja
 
Posts: 3
Joined: Tue Jan 17, 2017 10:53 am

Re: Physical size = 1.0

Postby mtbc » Wed Jan 18, 2017 12:33 pm

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
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