[3dem] Question regarding eer .gain files and defects

[Grigory Sharov]

Hi Philipp,

it seems that TFS has recently removed the XML string with defects from the
65100 tiff tag inside EER files. Besides looking for zero pixels in the
gain file another option is to check
C:/Titan/Data/EF-Falcon4/SensorDefects.xml file. 0,0 should be in the
bottom left corner.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gsharov at mrc-lmb.cam.ac.uk


On Thu, Jan 11, 2024 at 10:57 AM Philipp Sebastian Erdmann <
philipp.erdmann at fht.org> wrote:

> *Dear All,*
>
> I recently tried reading the defects from the .gain file of our Falcon4i.
>
> However, the xml embedded in the .gain reads as:
>
> <defects><!-- Defects file not present --></defects>
>
> Is the is bug in the software? Maybe it is not yet implemented by TFS?
>
> Are there other ways to extract it?
>
> I know the .gain zeros are the defects, but is this not an issue if you
> take the reciprocal?
>
> 1/0 = 🤯
>
> We’re trying to figure out which software does best in processing .eer
> files of tomograms.
>
> (Low dose; ca 3 e/Å2)
>
> Relion looks perfect but does not produce 1/2 stacks for denoising.
>
> Warp and MC3 produce 1/2 stacks, but I can see artifacts in the pixel
> substitution.
>
>
> Thanks for your help!
>
>
> Philipp.
>            ​
> Philipp Sebastian Erdmann
> Research Group Leader
> Erdmann Group,
> <https://urldefense.com/v3/__https://humantechnopole.it/en/research-groups/erdmann-group/__;!!Mih3wA!Cen_KzSXfQPgE9bJjRgu0iKxL-eaaIQFg-LOnFqxsjzOhNqCky6kT1AdE67gqJixPfoJKjjxCgwErbWqbL7Gz5S7r7Z9$>
> Structural Biology Research Centre
> Human Technopole
> Palazzo Italia
> Viale Rita Levi Montalcini, 1
> 20157 Milan, Italy
> M. +39 3452453710
> E. philipp.erdmann at fht.org
>
>
> <https://urldefense.com/v3/__https://www.facebook.com/htechnopole__;!!Mih3wA!Cen_KzSXfQPgE9bJjRgu0iKxL-eaaIQFg-LOnFqxsjzOhNqCky6kT1AdE67gqJixPfoJKjjxCgwErbWqbL7Gz_nSu4FY$>
>
> <https://urldefense.com/v3/__https://twitter.com/humantechnopole__;!!Mih3wA!Cen_KzSXfQPgE9bJjRgu0iKxL-eaaIQFg-LOnFqxsjzOhNqCky6kT1AdE67gqJixPfoJKjjxCgwErbWqbL7Gz78cWKM5$>
>
> <https://urldefense.com/v3/__https://www.linkedin.com/company/htechnopole__;!!Mih3wA!Cen_KzSXfQPgE9bJjRgu0iKxL-eaaIQFg-LOnFqxsjzOhNqCky6kT1AdE67gqJixPfoJKjjxCgwErbWqbL7GzxO2qN7j$>
> <https://urldefense.com/v3/__https://www.instagram.com/humantechnopole/__;!!Mih3wA!Cen_KzSXfQPgE9bJjRgu0iKxL-eaaIQFg-LOnFqxsjzOhNqCky6kT1AdE67gqJixPfoJKjjxCgwErbWqbL7Gz8t4KDaj$>
> Prima di stampare questa e-mail, pensa all’ambiente.
> Before printing this e-mail, think of the environment
> Legal Disclaimer
> The information contained in or accompanying this email and any attachment
> thereto, is intended solely for the use of the stated recipient(s) and may
> contain information that is confidential and/or privileged. Any
> dissemination, distribution or copying of this email and any attachment by
> anyone who is not the stated recipient is strictly prohibited. If you
> receive this message in error, please notify the sender immediately and
> delete the message and any attachment from your system without retaining a
> copy.
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240111/d90dbfca/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image112083.png
Type: image/png
Size: 701 bytes
Desc: not available
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240111/d90dbfca/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image847006.png
Type: image/png
Size: 680 bytes
Desc: not available
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240111/d90dbfca/attachment-0005.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image280898.png
Type: image/png
Size: 464 bytes
Desc: not available
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240111/d90dbfca/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image094151.png
Type: image/png
Size: 721 bytes
Desc: not available
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240111/d90dbfca/attachment-0007.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image970602.jpg
Type: image/jpeg
Size: 64981 bytes
Desc: not available
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240111/d90dbfca/attachment-0001.jpg>