Resources

  • Australian for Microscopy and Microanalysis Society

    Microscopy Society of America

    International Federation of Microscopy Societies

    Committee of Asia Pacific Societies for Microscopy

  • MyScope, microscopy tutorial (pre-requisite for one on one teaching at IHIC)

    Leica Science-Lab, tutorials, article about microscopy and applications

    EM University, large repository of knowledge on EM and cryoEM

    CryoEM101, videos and animation about the cryoEM workflow

  • Instruments and procedures SOP

    Instruments and procedure RA

  • Tolls you will need:

    Minimum kit:

    - 2 sets of Dumont tweezers style #5, non-magnetic

    - appropriate grids (see below)

    - grid storage

    Optional tools:

    - ThermoFisher Vitrobot or  Leica EMGP tweezers

    - Diamond knife for ultrathing sections (35 degres for standard sections, 45 degres for hard materials) and cryo ultrathin sections (IHIC will provide glass knives only)

    Recommanded grid types by application:

    - negative staining and small nanoparticles: 400 mesh carbon coated grids (copper)

    - plastic sections; 50-100 mesh formvar carbon coated grids (copper)

    - plastic section tomography: 200 mesh formavar carbon coated grids (copper)

    - immunolabelling: 100-200 mesh formvar carbon coated grids (gold, nickel or copper)

    - routine cryoEM (liposome/exosome/cubosomes/phages/bacteria ...): 300 mesh lacey carbon (copper)

    - single particle analysis: 1.2/1.3 (or smaller holes) UltraFoil (or equivalent).

  • If a map resolution is given the pixel size has been calibrated using ApoF or orientated gold , otherwise it is the standard TFS/Gatan calibration

    Krios Gatan K3  (likely to change slighty)

    Magnification (EFTEM mode)Pixel size (Å)Resolution of map used (Å)
    53,0001.63gold
    64,0001.32gold
    81,0001.0693.12
    105,0000.8332.33
    130,0000.658 1.74
    165,0000.5111.40

    Krios Falcon 4i

    MagnificationPixel size (Å)Resolution of map used (Å)
    75,0001.036gold
    96,0000.808gold
    120,0000.639gold
    155,0000.5071.49

    Arctica Falcon 4

    Magnification (EFTEM mode)Pixel size (Å)Resolution of map used (Å)
    92,0001.523.2
    120,0001.192.4
    150,0000.942.1
    190,0000.731.8

    Arctica Gatan K2 (legacy)

    Magnification (EFTEM mode)Pixel size (Å)Resolution of map used (Å)
    79,0001.713.5
    100,0001.332.7
    130,0001.032.3
    165,0000.7882.5

    Tecnai F30 CETA

    MagnificationPixel size (Å)
    4,70023.6
    9,40012
    12,0009.4
    15,5007.14
    20,0005.56
    23,0004.71
    31,0003.51
    39,0002.79
    59,0001.82
    78,0001.4
    93,0001.17
    115,0000.94
    200,0000.47
    230,0000.39

    Talos L120C

    MagnificationPixel size (Å)
    2,60054.4
    3,40041.9
    5,30026.4
    6,70021.4
    8,50016.9
    11,00013.4
    13,50010.5
    17,5008.2
    22,0006.4
    28,0005
    36,0004
    45,0003.1
    57,0002.44
    73,0001.90
    92,0001.51
    120,0001.18
    150,0000.92
    190,0000.72
    240,0000.56
    310,0000.44
    390,0000.34

  • SPA box size calculator

    SPA box size calculator

    Enter the imaging conditions and particle size to get the extraction box, including room for CTF delocalisation.

    Box size (nearest even integer)

  • cryoEM particle box matcher

    Match particle boxes across two datasets

    Enter the pixel size and extraction box of each dataset. The calculator finds a shared final pixel size and box size with the least possible downsampling. Each dataset is cropped in real space and Fourier space, in whichever order loses the least.

    Dataset A
    Dataset B

    Pixel size tolerance between the two datasets: fixed at 0.0001 Å

    How it works

    Two kinds of crop are available. A real-space crop from box a to b keeps the pixel size and shrinks the field of view. A Fourier crop from a to b keeps the field of view and changes the pixel size by a / b. A pipeline for one dataset is an alternating sequence of up to four such steps in any order (for example real, Fourier, real, Fourier). Consecutive crops of the same kind merge into one, so alternating sequences cover everything. The final field of view only depends on the final box and pixel size, so extra steps do not lose more field of view. They make more integer box combinations reachable, which allows a larger final box for the same pixel size.

    The larger-pixel-size dataset is only cropped in real space, which keeps its pixel size untouched. For each candidate final box, from the largest downward, the search looks for a pipeline for the other dataset that reaches the same pixel size within 0.0001 Å. It takes the largest final box that works and, for that box, the pipeline with the fewest steps. If no such pipeline exists, it falls back to two-step pipelines for both datasets with a slightly larger final pixel size. Padding is never used.