https://home.cryonav.org/index.php?action=history&feed=atom&title=CryoNAV_Integration_CryoEM_ToolsCryoNAV Integration CryoEM Tools - Revision history2026-06-24T19:11:14ZRevision history for this page on the wikiMediaWiki 1.43.1https://home.cryonav.org/index.php?title=CryoNAV_Integration_CryoEM_Tools&diff=86&oldid=prevAdmin: Bot edit via cryonavedit.py: migrate to sidebar-target titles2026-05-20T20:31:17Z<p>Bot edit via cryonavedit.py: migrate to sidebar-target titles</p>
<p><b>New page</b></p><div>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.<br />
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== IMOD ==<br />
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The IMOD software package (Kremer et al., 1996; Mastronarde & Held, 2017) provides the core processing utilities CryoNAV invokes:<br />
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* '''alignframes''' -- motion correction<br />
* '''ctfplotter''' -- CTF estimation<br />
* '''tiltalign''' -- tilt series alignment<br />
* '''newstack''' -- image stack manipulation<br />
* '''tilt''' -- tomographic reconstruction<br />
* '''3dmod''' -- 3D viewer, launched as an external application for volume inspection and model building (see [[CryoNAV Grid Visualization Tools#3D visualization via 3dmod|3D visualization via 3dmod]])<br />
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IMOD must be installed on the execution host(s) for processing steps to run.<br />
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== CryoCARE ==<br />
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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.<br />
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== DeepDeWedge ==<br />
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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.<br />
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== Acquisition software detection ==<br />
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CryoNAV's [[CryoNAV Tilt Series Data Collection Import|SmartScan]] import engine currently recognizes folder structures produced by:<br />
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* '''SerialEM'''<br />
* '''Thermo Fisher EPU'''<br />
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Additional acquisition-software support can be added through the modular detection framework.<br />
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== Execution backends ==<br />
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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 [[CryoNAV Overview Tomogram Processing#Local and HPC execution|Local and HPC execution]].<br />
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== See also ==<br />
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* [[CryoNAV Overview Tomogram Processing|Tomogram Processing Overview]]<br />
* [[CryoNAV Grid Visualization Tools|Grid Visualization]]<br />
* [[References]]<br />
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[[Category:Processing]]</div>Admin