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TOM Toolbox
Elaborates data acquisition schemes with autotuning functions and sophisticates image analysis routines. TOM Toolbox integrates established algorithms and concepts tailored to the special needs of low dose electron tomography (ET). It provides three-dimensional images not only of periodic or repetitive objects, but also of structures with unique topologies. The software represents a way of working with the electron microscope and can serve as the basis for high-throughput applications.
UCSF Tomography
Collects single-axis tilt series on electron transmission microscopes. UCSF Tomography is a software that was implemented based upon an approach in which the compustage tilting is modeled as geometric rotation. The spatial movement of the sample as a result of stage tilting can be predicted based upon previously collected tomographic images. It has been proven to be very robust in collecting cryo tilt series on thin and thick samples at various magnifications up to 60,000x.
TCCC / Thresholded Constrained Cross-Correlation
Improves results for Signal-to-Noise Ratios (SNR) lower than 0.1. TCCC allows to analyze macromolecules in thicker samples like whole cell or lower the defocus in thinner samples to push the first zero of the Contrast Transfer Function (CTF). TCCC uses statistics of the noise to automatically select only a small percentage of the Fourier coefficients to compute the cross-correlation. The thresholding has two main advantages in the cross-correlation score: first, reduces the influence of the noise; second, avoids the missing wedge normalization problem since we consider the same amount of coefficients for all possible pairs of subtomograms.
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