[3dem] Way to read raw pixel size from .eer?

[Ioannis Skalidis]

Thanks Takanori!

Running 'strings xxx.eer | less | grep sensor' actually contains the 
field below:

item name="sensorPixelSize.width" unit="m">8.85268664e-11

which seems to display the correct pixel size for the acquisition. I 
cross-validated it with data from multiple acquisitions and it always 
changes accordingly.


On 21.07.23 14:54, Takanori Nakane wrote:
> Hi,
>
> EER files contain some metadata in TFS-specific
> extended TIFF tags (e.g. IFD 65001).
> You have to write a script to read it but a dirty way is to just run
>
> strings XXX.eer | less
>
> and go to the bottom.
>
> There is a "sensorPixelSize.height" field.
> But I guess this is a physical pixel size of the detector
> independent of the magnification.
> I don't know if EER contains the pixel size at the sample.
>
> Best regards,
>
> Takanori Nakane
>
> On 2023/07/21 21:46, Ioannis Skalidis wrote:
>> Dear all,
>>
>> I was looking for the raw pixel size of some acquired data and 
>> realized that when I use the 'header' command from the 3dmod package 
>> with the -eer modifier to read the header of an .eer file, it always 
>> returns a pixel spacing of 1 Å. Of course, I can read the header of 
>> the corresponding .mrc files that are generated, but I was thinking 
>> if there is a way in unix/macos environments to read the .eer 
>> metadata directly. Does anybody have a way to do this?
>>
>> Thanks,
>>
>> Ioannis.
>>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem

-- 
Dr. rer. nat. Ioannis Skalidis
Biochemistry & Cryo-EM Scientist
Post-doctoral researcher
Kastritis Laboratory for Biomolecular Research
Cryo-Electron Microscopy & Computational Structural Biology

________________________________________________
Martin-Luther-Universität Halle-Wittenberg
Biozentrum, Room A.2.21
IWE ZIK HALOmem NWG III
"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
Weinbergweg 22, 06120 Halle
tel: +49 345 5524986
web (Lab): https://urldefense.com/v3/__https://blogs.urz.uni-halle.de/kastritislab/__;!!Mih3wA!Hb9v9wn1_7L0-Ym0Y6T4t5f0Y4PuT4U9kZVq7e4rM8XQ2SL3SdUcSp8_KbbCiK1VarWOjpRUgoEjFu32h24oJtDV$ 
web (HALOmem): https://urldefense.com/v3/__https://www.halomem.de/en/__;!!Mih3wA!Hb9v9wn1_7L0-Ym0Y6T4t5f0Y4PuT4U9kZVq7e4rM8XQ2SL3SdUcSp8_KbbCiK1VarWOjpRUgoEjFu32h9EZCEz2$