View source for Integration with Cryo-EM 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 [[Grid Visualization#3D visualization via 3dmod|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 [[Tilt Series Data Import|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 [[Tomogram Processing Overview#Local and HPC execution|Local and HPC execution]].

== See also ==

* [[Tomogram Processing Overview]]
* [[Grid Visualization]]
* [[References]]

[[Category:Processing]]