CryoNAV Integration CryoEM Tools
CryoNAV does not implement its own reconstruction algorithms. Instead, it wraps established command-line tools and provides a unified interface, parameter management, and progress tracking on top of them.
IMOD
The IMOD software package (Kremer et al., 1996; Mastronarde & Held, 2017) provides the core processing utilities CryoNAV invokes:
- alignframes -- motion correction
- ctfplotter -- CTF estimation
- tiltalign -- tilt series alignment
- newstack -- image stack manipulation
- tilt -- tomographic reconstruction
- 3dmod -- 3D viewer, launched as an external application for volume inspection and model building (see 3D visualization via 3dmod)
IMOD must be installed on the execution host(s) for processing steps to run.
CryoCARE
CryoCARE (Buchholz et al., 2019) provides content-aware image restoration for cryo-EM data. CryoNAV constructs CryoCARE invocations from template parameters and runs them via the same Executor interface used for IMOD jobs.
DeepDeWedge
DeepDeWedge (Wiedemann & Heckel, 2024) is a deep-learning method for simultaneous denoising and missing-wedge reconstruction in cryogenic electron tomography. CryoNAV supports DeepDeWedge through the same template-based job submission system.
Acquisition software detection
CryoNAV's SmartScan import engine currently recognizes folder structures produced by:
- SerialEM
- Thermo Fisher EPU
Additional acquisition-software support can be added through the modular detection framework.
Execution backends
Job execution is abstracted behind an Executor interface with SLURM and local-subprocess implementations, both of which can be active simultaneously in a single deployment. See Local and HPC execution.