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| 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.
| | #REDIRECT [[CryoNAV Integration CryoEM Tools]] |
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| == IMOD ==
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| The IMOD software package (Kremer et al., 1996; Mastronarde & Held, 2017) provides the core processing utilities CryoNAV invokes:
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| * '''alignframes''' -- motion correction
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| * '''ctfplotter''' -- CTF estimation
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| * '''tiltalign''' -- tilt series alignment
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| * '''newstack''' -- image stack manipulation
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| * '''tilt''' -- tomographic reconstruction
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| * '''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]])
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| IMOD must be installed on the execution host(s) for processing steps to run.
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| == CryoCARE ==
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| 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.
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| == DeepDeWedge ==
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| 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.
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| == Acquisition software detection ==
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| CryoNAV's [[Tilt Series Data Import|SmartScan]] import engine currently recognizes folder structures produced by: | |
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| * '''SerialEM'''
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| * '''Thermo Fisher EPU'''
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| Additional acquisition-software support can be added through the modular detection framework.
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| == Execution backends ==
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| 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]].
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| == See also ==
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| * [[Tomogram Processing Overview]]
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| * [[Grid Visualization]]
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| * [[References]]
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| [[Category:Processing]]
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