Tutorial: EER File Support

Electron-event representation (EER)

CryoSPARC supports reading input movies in electron-event representation (EER) format. EER is a special format developed by Thermo Fisher Scientific currently used for output from Falcon4 cameras. EER records individual electron detection events rather than storing movies as a series of image frames. For more information, please see Guo et al., Electron-event representation data enable efficient cryoEM file storage with full preservation of spatial and temporal resolution (IUCrJ).

Importing EER data

When importing EER data for processing in cryoSPARC, there are two additional parameters that must be specified in Import Movies jobs and in the Session Configuration panel in cryoSPARC Live.

EER-specific import parameters (Import Movies)

CryoSPARC converts the electron events recorded in an EER file into a stack of images, similar to what would be found in an MRC or TIFF file. The "EER Number of Fractions" parameter determines how many "fractions" are in the resulting movie. Too many fractions can result in very large memory demands during motion correction and longer processing times, while too few fractions can result in inadequate motion compensation. The default value of 40 is suitable in many cases.

The "EER Upsampling Factor" allows the rasterized images to have a higher resolution than the actual resolution of the camera (similar to super-resolution images from Gatan cameras). For example, an upsampling factor of 2 will create an image with twice as many pixels in each direction as the physical camera. Values of 1 (no upsampling/native resolution), 2 and 4 are supported. Note that using a value of 4 may result in extremely large images and high GPU memory requirements. In some cases, it is possible to recover information beyond the physical Nyquist resolution of the camera using upsampling of e.g., 2.