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

[Ludtke, Steven J.]

conda activate eman2

e2iminfo.py file.eer --header


0.

EER.acquisition_id: 20230523.193352.415

EER.camera_name: BM-Falcon

EER.commercial_name: Falcon 4

EER.compression: 65001

EER.eer_gain_reference: ImagesForProcessing/BM-Falcon/200kV/20230518_180445_EER_GainReference.gain

EER.exposure_time: 0.99720799999999998

EER.mean_dose_rate: 7.4649417694525013

EER.number_of_frames: 238

EER.sensor_image_height: 4096

EER.sensor_image_width: 4096

EER.sensor_pixel_size.height: 7.39449266e-11

EER.sensor_pixel_size.width: 7.39449266e-11

EER.serial_number: 20-35-A0X-XST

EER.timestamp: 2023-05-23T19:33:52.915710-05:00

EER.total_dose: 7.384066590322254

HostEndian: little

ImageEndian: little

apix_x: 1.0

apix_y: 1.0

apix_z: 1.0

changecount: 0

datatype: 7

is_complex: 0

is_complex_ri: 1

is_complex_x: 0

nx: 4096

ny: 4096

nz: 1

source_n: 0

source_path: Supervisor_20230523_190932_81_PRAFrac1_ultraufoil/Images-Disc1/GridSquare_23254874/Data/FoilHole_24224148_Data_24223466_24223468_20230523_193352_EER.eer


Should work for any CryoEM file format to get header information. For most formats the A/pix information would wind up in apix_x, but it looks like this hasn't been implemented in EER at the moment. Will have to fix that...

For programmatic work from Python:

python
from EMAN2 import *
img=EMData("file.eer",0) # 0 is the first image in the stack
print(img["EER.sensor_pixel_size.height"])

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke at bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology         Dept. of Biochemistry
Deputy Director, Advanced Technology Cores                and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

On Jul 21, 2023, at 8:08 AM, Takanori Nakane <tnakane.protein at OSAKA-U.AC.JP> wrote:

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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