CryoNAV Download - Revision history

Admin: Bot edit via cryonavedit.py: migrate to sidebar-target titles

2026-05-20T20:30:15Z

Bot edit via cryonavedit.py: migrate to sidebar-target titles

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-=Download=
+CryoNAV is in active development and is not yet available for download. This page will be updated when the first public release is announced.
-CryoNAV is currently under development and not yet available for public download. However, the software is designed to integrate with various established cryo-EM tools. Below are the download links for the cryo-EM software packages that CryoNAV is planned to work with:
+For the current status, see the [[CryoNAV About#Status and roadmap|Status and roadmap]] section.
-==Core Cryo-EM Processing Tools==
+[[Category:Getting Started]]

Admin at 22:12, 20 June 2025

2025-06-20T22:12:44Z

← Older revision		Revision as of 00:12, 21 June 2025
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	* '''Download:''' https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt		* '''Download:''' https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt
	* '''Description:''' Program for finding CTFs of electron micrographs, developed by the Grigorieff Lab		* '''Description:''' Program for finding CTFs of electron micrographs, developed by the Grigorieff Lab


	===RELION===		===RELION===
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	* '''GitHub:''' https://github.com/cryoem/eman2		* '''GitHub:''' https://github.com/cryoem/eman2
	* '''Description:''' Comprehensive greyscale image processing suite for transmission electron microscopy data		* '''Description:''' Comprehensive greyscale image processing suite for transmission electron microscopy data

	==AI and Deep Learning Tools==		==AI and Deep Learning Tools==

Admin at 22:12, 20 June 2025

2025-06-20T22:12:18Z

← Older revision		Revision as of 00:12, 21 June 2025
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	* '''Download:''' https://bio3d.colorado.edu/imod/download.html		* '''Download:''' https://bio3d.colorado.edu/imod/download.html
	* '''Description:''' Comprehensive software for processing cryo-electron tomographic data and generating 3D reconstructions		* '''Description:''' Comprehensive software for processing cryo-electron tomographic data and generating 3D reconstructions

			===Dynamo===
			Subtomogram averaging and cryo-ET processing software.
			* '''Download:''' https://www.dynamo-em.org/
			* '''Description:''' Flexible development tool for cryo-ET data processing with high-performance computing support

			===CTFfind===
			Contrast transfer function estimation for electron micrographs.
			* '''Download:''' https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt
			* '''Description:''' Program for finding CTFs of electron micrographs, developed by the Grigorieff Lab


	===RELION===		===RELION===
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	===EMAN2===		===EMAN2===
	Scientific image processing suite with focus on cryo-EM and cryo-ET.		Scientific image processing suite with focus on cryo-EM and cryo-ET.
	* '''Download:''' https://blake.bcm.edu/emanwiki/EMAN2
	* '''GitHub:''' https://github.com/cryoem/eman2		* '''GitHub:''' https://github.com/cryoem/eman2
	* '''Description:''' Comprehensive greyscale image processing suite for transmission electron microscopy data		* '''Description:''' Comprehensive greyscale image processing suite for transmission electron microscopy data

	~~===Dynamo===~~
	~~Subtomogram averaging and cryo-ET processing software.~~
	* '''Download:''' https://www.dynamo-em.org/
	* '''Description:''' Flexible development tool for cryo-ET data processing with high-performance computing support

	~~===CTFfind===~~
	~~Contrast transfer function estimation for electron micrographs.~~
	* '''Download:''' https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt
	* '''Description:''' Program for finding CTFs of electron micrographs, developed by the Grigorieff Lab

	==AI and Deep Learning Tools==		==AI and Deep Learning Tools==

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	* Python environments (Anaconda/Miniconda recommended)		* Python environments (Anaconda/Miniconda recommended)

	CryoNAV ~~can~~ also ~~integrate~~ with SLURM for ~~processing~~ and S3 ~~bucket~~ for data retrieval.		CryoNAV also provides integration with SLURM for cluster computing and Amazon S3 for cloud-based data storage and retrieval.

	'''Important:''' Always check the specific system requirements and installation instructions for each software package before downloading. Many tools have dependencies on specific versions of libraries, compilers, or GPU drivers.		'''Important:''' Always check the specific system requirements and installation instructions for each software package before downloading. Many tools have dependencies on specific versions of libraries, compilers, or GPU drivers.

Admin: Created page with "=Download= CryoNAV is currently under development and not yet available for public download. However, the software is designed to integrate with various established cryo-EM tools. Below are the download links for the cryo-EM software packages that CryoNAV is planned to work with: ==Core Cryo-EM Processing Tools== ===IMOD=== Image processing and 3D reconstruction package for electron tomography. * '''Download:''' https://bio3d.colorado.edu/imod/download.html * '''Descr..."

2025-06-20T22:09:24Z

Created page with "=Download= CryoNAV is currently under development and not yet available for public download. However, the software is designed to integrate with various established cryo-EM tools. Below are the download links for the cryo-EM software packages that CryoNAV is planned to work with: ==Core Cryo-EM Processing Tools== ===IMOD=== Image processing and 3D reconstruction package for electron tomography. * '''Download:''' https://bio3d.colorado.edu/imod/download.html * '''Descr..."

New page

=Download=

CryoNAV is currently under development and not yet available for public download. However, the software is designed to integrate with various established cryo-EM tools. Below are the download links for the cryo-EM software packages that CryoNAV is planned to work with:

==Core Cryo-EM Processing Tools==

===IMOD===
Image processing and 3D reconstruction package for electron tomography.
* '''Download:''' https://bio3d.colorado.edu/imod/download.html
* '''Description:''' Comprehensive software for processing cryo-electron tomographic data and generating 3D reconstructions

===RELION===
REgularised LIkelihood OptimisatioN for cryo-EM structure determination.
* '''Download:''' https://relion.readthedocs.io/
* '''GitHub:''' https://github.com/3dem/relion
* '''Description:''' Empirical Bayesian approach for single-particle analysis and refinement of cryo-EM data

===EMAN2===
Scientific image processing suite with focus on cryo-EM and cryo-ET.
* '''Download:''' https://blake.bcm.edu/emanwiki/EMAN2
* '''GitHub:''' https://github.com/cryoem/eman2
* '''Description:''' Comprehensive greyscale image processing suite for transmission electron microscopy data

===Dynamo===
Subtomogram averaging and cryo-ET processing software.
* '''Download:''' https://www.dynamo-em.org/
* '''Description:''' Flexible development tool for cryo-ET data processing with high-performance computing support

===CTFfind===
Contrast transfer function estimation for electron micrographs.
* '''Download:''' https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt
* '''Description:''' Program for finding CTFs of electron micrographs, developed by the Grigorieff Lab

==AI and Deep Learning Tools==

===cryoCARE===
Content-aware image restoration for cryo-electron tomography.
* '''Download:''' https://pypi.org/project/cryoCARE/
* '''Description:''' Self-supervised deep learning approach for denoising cryo-electron tomographic data

===DeepDeWedge===
Deep learning for denoising and missing wedge reconstruction.
* '''Download:''' https://github.com/MLI-lab/DeepDeWedge
* '''Description:''' Self-supervised deep learning method for simultaneous denoising and missing wedge reconstruction in cryo-ET

==Installation Notes==

'''Prerequisites:''' Most cryo-EM software packages require:
* Linux or macOS operating systems
* CUDA-compatible GPUs for accelerated processing (recommended)
* MPI libraries for parallel processing
* Python environments (Anaconda/Miniconda recommended)

CryoNAV can also integrate with SLURM for processing and S3 bucket for data retrieval.

'''Important:''' Always check the specific system requirements and installation instructions for each software package before downloading. Many tools have dependencies on specific versions of libraries, compilers, or GPU drivers.

'''Academic Use:''' Most of these tools are freely available for academic research. Commercial users should check licensing requirements for each package.

==Support and Documentation==

For CryoNAV-specific questions about planned integrations with these tools, please contact Paula Navarro (paula.navarro{at}unil.ch).

For issues with individual software packages, please refer to their respective documentation, forums, or support channels linked on their download pages.

==See Also==
* [[Installation Guide]]
* [[Integration with Cryo-EM Tools]]
* [[Getting Started Home|Getting Started]]