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.xml metadata and pixel dimensions

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Please note:
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.

.xml metadata and pixel dimensions

Postby GaetanoLombardi » Tue Jan 24, 2017 10:23 am

Hi to everyone.

I have a lot of .tiff images from a confocal microscope. Each image has a .xml file. The tags included in these files are a little different from the standard OME (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1175959/). 

I need to calibrate MCiD Analysis and set pixel dimensions to obtain correct measurements. I think the useful tags are 


- <Distance Id="X">
<Value>2.1972656236198625E-08</Value>
</Distance>

- <Distance Id="Y">
<Value>2.1972656236198625E-08</Value>
</Distance>


but I don't know how to interpret them (pixel per micron?; micron per pixel?) Can someone help me?

Thank you to everyone.
---------------------------------------------------
Gaetano Lombardi, MD
Medicine School
University of Campania "Luigi Vanvitelli"
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Re: .xml metadata and pixel dimensions

Postby sbesson » Wed Jan 25, 2017 11:01 am

Hi,

as you can see from this table, there are quite a few formats using a combination of XML and TIFF formats. Do you have more information about the nature of the microscope and software used for acquiring the images?
Have you tried opening your data using Bio-Formats to see if the fileset is detected as one of the existing file formats and the metadata is parsed?

Best,
Sebastien
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sbesson
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