Difference between revisions of "Integration Commands"
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| − | == List of | + | == List of Integrated Commands == |
| − | Here, we show the list of | + | Here, we show the list of Integrated Commands provided in [[Eos]]. Currently, most of them is written by Makefile or bash. We will provide those written by [[PIONE]] in the near future. |
| − | ===[[Image Correction]] | + | ===[[Image Correction]]=== |
| − | ===[[Single particle analysis]] | + | ====[[CTF Correction]]==== |
| − | === | + | Main items described in the CTF Correction are the following: |
| − | === | + | |
| − | ===[[Electron tomography]] | + | Apply [[CTF Correction]] to [[tiff]] files: ([[:Media:Makefile-CTFCorrection.zip|Makefile only ]]) ([https://sourceforge.jp/projects/eos/scm/git/tutorial/archive/master/CTFCorrection/CTFCorrection1/ all files])<br> |
| − | ===[[Helical Symmetry analysis]] | + | *Use: [[CTF Correction#Example 1 CTF-compensation using Makefile]]<br> |
| + | [[CTF Correction]] using an input file : ([[:Media:Makefile-CTFCorrection2.zip|Makefile only]]) | ||
| + | ([https://sourceforge.jp/projects/eos/scm/git/tutorial/archive/master/CTFCorrection/CTFCorrection2/ all files])<br> | ||
| + | *Use 1: [[CTF Correction#Example 2 CTF correction using Makefile-2]]<br> | ||
| + | *Use 2: [[CTF Correction#Example 3 CTF effects on the Siemens star]]<br> | ||
| + | *Use 3: [[CTF Correction#Example 4 CTF influence on images with noises]]<br> | ||
| + | Compare the CTF-corrected images of a field with different amount of defocus: ([[:Media:Makefile-CTFCorrection4.zip|Makefile only]]) ([https://sourceforge.jp/projects/eos/scm/git/tutorial/archive/master/CTFCorrection/CTFCorrection4/ all files])<br> | ||
| + | This command requires the following command. ([[:Media:Makefile-LoopCommand.zip|Makefile only]]) ([https://sourceforge.jp/projects/eos/scm/git/tutorial/archive/master/TIPS/LoopCommand/ all files]) | ||
| + | *Use: [[CTF Correction#Example 5 defocus influence on images]]<br> | ||
| + | Do [[CTF Correction]] using two input files for images of a field with different amount of defocus.: ([[:Media:Makefile-CTFCorrection3.zip|Makefile only]]) ([https://sourceforge.jp/projects/eos/scm/git/tutorial/archive/master/CTFCorrection/CTFCorrection3/ all files])<br> | ||
| + | *Use 1: [[CTF Correction#Example 6 Averaging of images with different amounts of defocus]]<br> | ||
| + | *Use 2: [[CTF Correction#Example 7 Averaging of images with different amount of defocus 2]]<br> | ||
| + | <br> | ||
| + | |||
| + | ===[[Single particle analysis]]=== | ||
| + | ====[[Classification of 2D images|Classification of 2D images (Cluster analysis) and getting of average image]]==== | ||
| + | ====[[3D Reconstruction1|Estimation of projection angle using reference]]==== | ||
| + | ====[[3D Reconstruction2|Helical Single particle analysis]]==== | ||
| + | |||
| + | ===[[Electron tomography]]=== | ||
| + | ====[[3D Reconstruction3|Electron tomography method by using multiple ROI files]]==== | ||
| + | ===[[Helical Symmetry analysis]]=== | ||
| + | ====[[3D Reconstruction4|3D Reconstruction by Helical Symmetry]]==== | ||
===[[2D Image Processing]]=== | ===[[2D Image Processing]]=== | ||
===[[3D Image Processing]]=== | ===[[3D Image Processing]]=== | ||
Latest revision as of 04:17, 17 July 2017
Contents
List of Integrated Commands
Here, we show the list of Integrated Commands provided in Eos. Currently, most of them is written by Makefile or bash. We will provide those written by PIONE in the near future.
Image Correction
CTF Correction
Main items described in the CTF Correction are the following:
Apply CTF Correction to tiff files: (Makefile only ) (all files)
CTF Correction using an input file : (Makefile only)
(all files)
- Use 1: CTF Correction#Example 2 CTF correction using Makefile-2
- Use 2: CTF Correction#Example 3 CTF effects on the Siemens star
- Use 3: CTF Correction#Example 4 CTF influence on images with noises
Compare the CTF-corrected images of a field with different amount of defocus: (Makefile only) (all files)
This command requires the following command. (Makefile only) (all files)
Do CTF Correction using two input files for images of a field with different amount of defocus.: (Makefile only) (all files)
- Use 1: CTF Correction#Example 6 Averaging of images with different amounts of defocus
- Use 2: CTF Correction#Example 7 Averaging of images with different amount of defocus 2
