<div dir="ltr">Dear Tobias and the community,<div><br></div><div>Concerning your question, I just want to add some details about the "calibration samples".</div><div><br></div><div>Generally we have 3 types of samples for any calibration. (1) Calibration check samples (2) Reference material samples and (3) Certified reference material samples.</div><div><br></div><div>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.</div><div><br></div><div>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.</div><div>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.</div><div><br></div><div>Here are a list of commercially available recommended reference materials for TEM calibration:<br></div><div><div><br></div><div>1- Gold on Carbon: TedPella 613 or Agar AGS132</div><div>2-
Oriented Gold film: Tedpella 646 or Agar AGS135
</div><div>3-
Thalium Chloride: Agar AGS110 </div><div>4- Aluminum: TedPella 619 or Agar AGS108</div></div><div><br></div><div>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. <br></div><div><br></div><div>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: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Accuracy-5Fand-5Fprecision&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=RfdeS-TQzO2F0ARd76gPxIyzE0QL-rg2QnpXF8AAKbc-ms-uD2B_f7t1zGI09J61&s=Re9r7jublSwYNOC_gKrHoa33T7_LehPBPVbkMaZqJMk&e=">Accuracy and precision - Wikipedia</a>). Such beads can be ordered from the 2SPI catalog.</div><div><div><br></div></div><div>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 <b>ISO 29301:2017</b> 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.</div><div><br></div><div>Hope the community finds these comments useful.</div><div><br></div><div>Best Regards,</div><div><br></div><div><span style="color:rgb(0,0,0)">Farzad Hamdi, Dr.-Ing</span><br></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div style="color:rgb(0,0,0)">Scientist,</div><div style="color:rgb(0,0,0)">Kastritis Laboratory for Biomolecular Research</div><div style="color:rgb(0,0,0)"><span style="font-family:Helvetica,Arial,sans-serif;font-size:13px">Interdisciplinary research center HALOmem, </span></div><div style="color:rgb(0,0,0)"><span style="font-family:Helvetica,Arial,sans-serif;font-size:13px">Institute of Biochemistry and Biotechnology, </span><span style="font-family:Helvetica,Arial,sans-serif;font-size:13px">Biocenter, </span></div><div style="color:rgb(0,0,0)"><span style="font-family:Helvetica,Arial,sans-serif;font-size:13px">Martin Luther University Halle-Wittenberg, Halle (Saale), Germany</span></div><div style="color:rgb(0,0,0)">----------------------------------------------------------------------------------------</div><div style="color:rgb(0,0,0)">Martin-Luther-Universität Halle-Wittenberg</div><div style="color:rgb(0,0,0)">Biozentrum, Room A.2.14 & 15</div><div style="color:rgb(0,0,0)">IWE ZIK HALOmem NWG III</div><div style="color:rgb(0,0,0)">"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"</div><div style="color:rgb(0,0,0)">Weinbergweg 22, 06120 Halle</div><div style="color:rgb(0,0,0)">Telefone:</div><div style="color:rgb(0,0,0)">Office: +49 345 5524984</div><div style="color:rgb(0,0,0)">Glacios Room: +49 345 5524883</div><div style="color:rgb(0,0,0)">JEM-3200FSC Room: +49 345 5524868 </div><div style="color:rgb(0,0,0)">Cellphone: +49-1525-6841873</div><div style="color:rgb(0,0,0)">Web (Lab): <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__blogs.urz.uni-2Dhalle.de_kastritislab_&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=RfdeS-TQzO2F0ARd76gPxIyzE0QL-rg2QnpXF8AAKbc-ms-uD2B_f7t1zGI09J61&s=0FyWxzr_UsV5hXzTTTs7nVc0gN3p771nNbHibdwS0wI&e=" target="_blank">https://blogs.urz.uni-halle.de/kastritislab/</a></div><div style="color:rgb(0,0,0)">Web (HALOmem): <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.halomem.de_en_&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=RfdeS-TQzO2F0ARd76gPxIyzE0QL-rg2QnpXF8AAKbc-ms-uD2B_f7t1zGI09J61&s=XaDX1-vbVQVGydxrMcc7nj8AHF40WOrNFjULGCCZCbE&e=" target="_blank">https://www.halomem.de/en/</a></div><div><br></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jan 3, 2022 at 3:54 PM Tobias Furstenhaupt <<a href="mailto:furstenh@mpi-cbg.de">furstenh@mpi-cbg.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear colleagues,<br>
<br>
I would like to check/correct the pixelsize on our TEMs and am open for suggestions to make my life as easy as possible.<br>
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.<br>
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.<br>
<br>
Does anybody have better suggestions, procedures or calibration standards that work well?<br>
<br>
thanks alot in advance :)<br>
Tobias <br>
<br>
<br>
----------------------------------- <br>
Tobias Fürstenhaupt, PhD <br>
head of Electron Microscopy <br>
Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) <br>
Pfotenhauerstrasse 108 <br>
01307 Dresden, Germany <br>
<br>
mail: <a href="mailto:furstenh@mpi-cbg.de" target="_blank">furstenh@mpi-cbg.de</a> <br>
phone: (+49) (0)351 210-2690 <br>
cell: (+49) (0)176 / 44498706 (NEW!)<br>
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</blockquote></div>