[3dem] 'easy' (re)calibration of pixelsize?

Tue Jan 4 05:38:56 PST 2022

Dear Tobias and the community,

Concerning your question, I just want to add some details about the
"calibration samples".

Generally we have 3 types of samples for any calibration. (1) Calibration
check samples (2) Reference material samples and (3) Certified reference
material samples.

Sample type 1 are those made for verifying if your previous calibrations
are already correct or not. These samples do not offer any fundamental
physical parameter and are made to represent a "generally trustable
dimension" kinda indirectly! They have no accuracy/precision guarantee or
traceability to any standard institution etc. For TEM magnification
calibration, cross grating and shadowed latex samples can be placed in this
category. The mold for making cross grating replicas is made using a known
laser wavelength but the stability and changes of the replica film during
the preparation is not verified in any standard institute/lab like NIST or
BAM etc. and we just trust them.

Sample type 2 are those representing a defined physical or natural
dimension which are globally constant around the world such as d-spacing
of pure crystals or certain laser wavelengths etc. and are measured
many times by reputable organizations.
In TEM calibration context pure compounds such as Au, Pt, Pd, ... and
compounds such as TlCl, Refractory metal carbides, etc. are in this
category. It is worthy of note that while searching for the parameters of
such materials some considerations must be taken into account such as the
sample temperature during calibration and vacuum condition etc. Another
noteworthy remark is that non-stoichiometric but pure alloys and compounds
such as Pd-Pt, Pt-Ir , Si-Ge or evaporated silicon oxides etc. are
definitely not reference materials and should not be used for this purpose.
For the definition of a stoichiometric or non-stoichiometric compound you
can ask a physical chemist or a materials scientist with some knowledge of
phase diagrams or thermodynamics of solutions and mixtures.

Here are a list of commercially available recommended reference materials
for TEM calibration:

1- Gold on Carbon: TedPella 613 or Agar AGS132
2- Oriented Gold film: Tedpella 646 or Agar AGS135
3- Thalium Chloride: Agar AGS110
4- Aluminum: TedPella 619 or Agar AGS108

Should you want to make your own sample, any refractory, chemically stable,
non-magnetic and pure compound is preferred. For example platinum group
members are ideal for this purpose. I am  also not aware if the
commercially available samples such as asbestos (Crocidolite), Copper
Phthalocyanine, graphitised carbon or protein particles (e.g. Ferritin or
Catalase 2D crystals) could also be considered as a reference material or
not as they are not very rigid crystals with very defined and constant
d-spacings. Also some samples like potassium chloroplatinate have specific
directionality which need high tilt to reveal the desired lattice fringes
and are not advisable. Generally speaking it is trivial that one should
avoid high defoci and also provide parallel beam (as much as possible)
while calibrating using lattice fringes.

Sample type 3 samples are those which are not fundamentally constant but
are already examined by a standard center and compared to another known
sample (either another reference or another certified reference material).
This method of hierarchical credibility and validation is named
traceability. In TEM context we have multilayer x-ray monochromators
(normally made using MBE or similar coating methods) or similar structures
made for this purpose such as BAM-L002/XXX or Norrox Scientific Mag*I*Cal.
BAM-L002-XXX is in the bulk form and needs to be prepared using a FIB-SEM.
Also, there are some traceable and calibrated beads (Latex, Glass, Silica
etc) which despite their traceability and high accuracy, do not offer high
precision (for better understanding of accuracy vs. precision please
see: Accuracy
and precision - Wikipedia
<https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Accuracy-5Fand-5Fprecision&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=RfdeS-TQzO2F0ARd76gPxIyzE0QL-rg2QnpXF8AAKbc-ms-uD2B_f7t1zGI09J61&s=Re9r7jublSwYNOC_gKrHoa33T7_LehPBPVbkMaZqJMk&e= >). Such beads can be
ordered from the 2SPI catalog.

If you are going to use your scope for high resolution CryoEM SPA, an
obsession for a super accurate or traceable calibration is really not
needed as there are many structural signatures in the structure that can be
used to correct the model after image processing and refinement and the
consequent model building. But if you intend to use your scope for
meterology applications, then it is necessary to have a look at *ISO
29301:2017* standard and use a sample type 2 or 3. Counter intuitively a
good calibration of a TEM in low mag is way more difficult that high mag.
In higher mag the image distortion is normally negligible and there are
many reference materials. In low mag however most machines suffer from
image distortion (especially those with energy filters) and also suitable
reference materials become scarce. Also if you use lens coupled cameras or
fiber optic coupled CCD (or CMOS) you should examine the image for any
possible optical distortion.

Hope the community finds these comments useful.

Best Regards,

Farzad Hamdi, Dr.-Ing
Scientist,
Kastritis Laboratory for Biomolecular Research
Interdisciplinary research center HALOmem,
Institute of Biochemistry and Biotechnology, Biocenter,
Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
----------------------------------------------------------------------------------------
Martin-Luther-Universität Halle-Wittenberg
Biozentrum, Room A.2.14 & 15
IWE ZIK HALOmem NWG III
"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
Weinbergweg 22, 06120 Halle
Telefone:
Office: +49 345 5524984
Glacios Room: +49 345 5524883
JEM-3200FSC Room: +49 345 5524868
Cellphone: +49-1525-6841873
Web (Lab): https://urldefense.proofpoint.com/v2/url?u=https-3A__blogs.urz.uni-2Dhalle.de_kastritislab_&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=RfdeS-TQzO2F0ARd76gPxIyzE0QL-rg2QnpXF8AAKbc-ms-uD2B_f7t1zGI09J61&s=0FyWxzr_UsV5hXzTTTs7nVc0gN3p771nNbHibdwS0wI&e= 
Web (HALOmem): https://urldefense.proofpoint.com/v2/url?u=https-3A__www.halomem.de_en_&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=RfdeS-TQzO2F0ARd76gPxIyzE0QL-rg2QnpXF8AAKbc-ms-uD2B_f7t1zGI09J61&s=XaDX1-vbVQVGydxrMcc7nj8AHF40WOrNFjULGCCZCbE&e= 

On Mon, Jan 3, 2022 at 3:54 PM Tobias Furstenhaupt <furstenh at mpi-cbg.de>
wrote:

> Dear colleagues,
>
> I would like to check/correct the pixelsize on our TEMs and am open for
> suggestions to make my life as easy as possible.
> For low mags I have the venerable crossgrating with a spacing of 463nm. My
> plan is to take images and use the cross-correlation function from
> DigitalMigrograph (DM) to get a precise spacing in pixels.
> For high and ultra-high mags I have the MAG*I*CAL that offers calibrated
> distances in the range of 10nm/100nm/1000nm/4um. Plan is to use Fiji or DM
> and do manual mesurements.
>
> Does anybody have better suggestions, procedures or calibration standards
> that work well?
>
> thanks alot in advance :)
> Tobias
>
>
> -----------------------------------
> Tobias Fürstenhaupt, PhD
> head of Electron Microscopy
> Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
> Pfotenhauerstrasse 108
> 01307 Dresden, Germany
>
> mail: furstenh at mpi-cbg.de
> phone: (+49) (0)351 210-2690
> cell: (+49) (0)176 / 44498706 (NEW!)
> _______________________________________________
> 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/20220104/50f6cdd3/attachment.html>