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

[Takanori Nakane]

Hi,

 > 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

Great! My files contained 0.000, perhaps because they were from
a test version of the detector software.

 >     et =  ET.XML(f.eer_metadata)

This is also great. I didn't know the tifffile package understands
non-standard TIFF tags.

Best regards,

Takanori Nakane

On 2023/07/21 22:03, Ioannis Skalidis wrote:
> 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.
>>>
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>