Main Page
Contents
- 1 Welcome to Eospedia
- 2 Over-all view of the system that we are now developing (Eos/PIONE/Zephyr & WITs/VEM system)
- 3 Beginner's Guid
- 4 Installation
- 5 Eos reference
- 6 Eos tutorial
- 7 Developers' Guide of Eos
- 8 Image Processing and Image Analysis
- 8.1 General Image Processing
- 8.1.1 Simple Image Processing
- 8.1.2 Input of image and Lens
- 8.1.3 CTF, PSF and MTF
- 8.1.4 Sampling
- 8.1.5 Quantization
- 8.1.6 Noise reduction
- 8.1.7 Edge extraction
- 8.1.8 Binarization
- 8.1.9 Image processing using the Fourier Space
- 8.1.10 Image processing using the Kernel of the Real space
- 8.1.11 Image processing using the Mathematical morphology
- 8.2 EM Image Processing
- 8.3 3D Reconstruction
- 8.1 General Image Processing
- 9 Electron Microscope
- 10 The future of Eos
- 11 FAQ and TIPS
- 12 Why we have been developing Eos/PIONE ?
- 13 Eos User Group
- 14 About a symbol mark of Eos
- 15 Tools and Sites related to Eos
- 16 External link
- 17 How to use mediawiki
Welcome to Eospedia
We started the new manual site of Eos for only few people at 05 Nov. 2010. And we started the operation of Eospedia closed β version of the laboratory. In August 2012, we opened as the head family of the home page of the electron microscope image processing system Eos here.
We would like to summarize extensive knowledges as description and algorithm of the command about Eos. Also We will summarize here in the same way for the PIONE (developing since 2012) and VEM/WITs (developing since 2013). In addition, we would like to operate as a site that is possible to learn including an electron microscope image processing, the basics of the various image processing here.
We are developing Eos on Eos@sourceforge, PIONE on PIONE@github. We would like to expand the information that summarizes them here. In the future, we are considering also be independent of the university. Try and take a look at this related sites If you are interested in any of the development and use of these. The philosophy of wiki is not "how do us prevent mistakes" but "how do us improve it". Therefore we are glad, if you write freely your know-how and knowledge without afraid to make mistakes (Of course, incoherence is out of the question.).
Old Eos pages are here.
Now this Eospedia is under construction. Eospedia.ja has also opend here. Japanese version of Eospedia has more information than this Eospedia in English.
In addition, there is a forum and mailing list for Eos. If you want to know how to use the Eos: eos-users@ If you are interested in the development of in Eos: eos-developers@ If you are able to help write the document of Eos: eos-document@ If you can cooperate, we are glad.
We opened "Eos User Group"[1] on the facebook futher. We would like to spread using this.
Please contact Yasunaga[2] for more information.
Over-all view of the system that we are now developing (Eos/PIONE/Zephyr & WITs/VEM system)
We are currently developing a new system, namely "Eos/PIONE/Zephyr & WITs/VEM system", which would provide a total solution for image acquisition, processing and analysis of electron microscopic data by taking care of a series of necessary workflows in the analysis. The system has integrated each system (Eos, PIONE, Zephyr & WITs and VEM) that were developed for specific stages in the EM data analysis, and therefore can be termed as "Systems of System". But below we start by describing the summary and purposes of each system.
You can find a summary description of the integrated system in Eos/PIONE/Zephyr/WITs/VEM system (Under construction)
Beginner's Guid
What is Eos ?
We here describe what is Eos.
How to use Eos Commands
We here describe commands of Eos by CUI.
How to use Eos by Makefile
We here describe how to integrate commands using make
List of command
We here show all of commands Eos supplies.
Functional order of Eos command list
We here show functional order of Eos commands.
Installation
Required Environment
Download
We here describe how to download Eos. We are currently developing a Eos at SourceForge.
How to install Eos
We here describe how to install Eos.
Installation of PIONE
We here describe how to install a new process flow control system, PIONE. PIONE has been developed on "github".
Eos reference
Integrated commands supplied by Eos
We here describe integration commands supplied by Eos, one of the support Eos supplies.
Integration comannd : PIONE
We here describe PIONE that is provided as an integrated environment that corresponds to the cloud environment and distributed environment by Eos.
Eos tutorial
How to set Eos environment
At first, we explain how to install Eos simplily. The details are described in Eos Installation.
How to use commands of Eos
We explain how to use Eos commands. In details, please refer to the Eos Commands. Eos perform image processing and analysis with CUI, normally, although some interactive tools have GUI. In the near-future, each command has GUI on a browser by javascript.
Image format on Eos
Image formats in Eos and how to transform image format from other general image formats are explained here.
Simple image processing using Eos
Simple image processing and analysis can be performed here.
Tutorial List
Here are Makefile and PIONE for Small Tools or several Image Processing.
CTF Correction
Electron micrographs were greatly modified in contrast due to how to take them. Here we show the correction methods of CTF.
Single particle analysis
This is a tutorial section of single particle analysis. Here we show the single particle analysis with reference. Actually, we must choose the 3D Reconstruction methods considering the situations.
Concept of Single particle analysis
Particle picking
At first, we pick particles from electron micrographs. Here, the manual picking method is shown, although automatic methods are also proposed.
Classification of 2D images
Next, we classify 2D-images following their shape and so average them per cluster to improve the ratio of signal to noise.
Estimation of projection angle using reference
Third, we determine the projection angle of each particle in the case of the presence of reference images, although the determination methods of projection angles are also proposed without reference.
Estimation of projection angle without using reference
As another way, we show the method of determining the projection angle of each particle in the case of not using reference images. Method of Common Line Search by Common Line is general.
3D Reconstruction: Backprojecdtion
Forth, we reconstruct 3D objects from 2D images, especially Backprojection.
Visualization tools
FInally, we interpret 3D objects reconstructed from 2D images using visualization tools.
Electron Tomography
Electron Tomography is one of the powerful techniques to solive 3D objects such as whole cell, cytoskeleton in cell, and protein structure with polymorphism. It reconstruct 3D objects from tilt-series images of the same photo field.
The overview of Electron Tomography
Electron Tomography can supply us 3D objects from tilt-series of 2D images of the same field. Here we explain the overview.
Image Correction
Fist, we must correct CTF (Contrast Transfer Function) becuase the 2D images are taken with larger defocusing values.
Rough Alignment
Next, we align 2D images roughly using correlation between each image.
Fine Alignment
Third, we estimate the tilt-axis position and angles.
3D Reconstruction
Fourth, we reconstruct 3D image from a set of tilt-series images.
Problems of Electron Tomography image
We must pay attention of misleading blurring due to missing area, which is generated from the limitation of projection angles.
Interpretation of 3D Reconstruction
Last, we must perform segmentation of 3D objects to interpret them. Thus we must use computer-aided visualization tools.
Averaging of Subtomograms
Tomogram images of cryo-microscopy include a lot of noise, thus it is required the averaging of the particles have the same structure.
Notes
This tutorial pages were created with refer to the documents used single particle workshop on 2012/09/10-11.
Developers' Guide of Eos
Eos System Architecture
For Eos System Developers
Eos System Commands
Eos development under Sourceforge
We here show a flow of development of Eos under Sourceforge: 1. create clone from Sourceforge, develop a new tool or object and finally register them into Sourceforge.
Development of small tools
How to create a small tool
How to create Small Tools(Command Group) is described.
Introduction of small tools
We introduce some simple examples of Small Tools(Command Group).
How to create API
How to carete Object-oriented library (API) is described。
API list
We show a list of Object-oriented library (API).
Functional order of API
We here show functionl oder of API (Object-oriented libraries) supplied by Eos.
How to create integration commands
We describe how to develop integration commands.
Integration by Makefile
Here how to integrate commands using Makefile are shown。Furthreore, Visualmake supply simple and easy GUI (Graphical User Interface).
Integration by PIONE
We here show how to integrate commands using PIONE, which is a rule-based process definition and work under distributed computing system.
PIONE tutorial
Here is the tutorial how to use PIONE.
PIONE tutorial-PNML
Here, describe how to design process definition document by using PIONE.
Integration by bash
bash etc.
Integration by integration commands
We here describe how to integrate commands by Display2, smolet, Eos etc. programed with Tcl/Tk, ctfDisplay etc. programed with Ruby/Tk,molvie etc. programmed by C-language.
Image Processing and Image Analysis
General Image Processing
Summarizing about the general image processing here.
Simple Image Processing
Tutorial on simple image processing using the Eos has been published.
Input of image and Lens
Before performing image processing using a computer, you should keep in mind about the input device that digitize images.
CTF, PSF and MTF
True image: f(x,y) is degraded due to the method of Input of image and performance of the Lens.
Sampling
To convert analog images to digital images, it is important that discretize the space by decomposing. This step is called Sampling.
Quantization
First, in digital image process the operation that expresses density values within certain number of bits (Optical density) is required. This operation is called quantization(AD convert).
Noise reduction
In order to deal the image including a lot of noise, knowing well the nature of the noise is important.
Smoothing
This is an image processing method with the primary purpose of eliminating the noise in the image. By understanding well the nature of the noise, the noise can be reduced properly.
Edge extraction
This is an important step in order to understand the shape of the object, but it is also a very difficult step.
Binarization
This is the process of isolating the background and the signal, and extracting the representative point and the skeletal. And it is the start process of the analysis and image processing.
Image processing using the Fourier Space
Image processing using the Kernel of the Real space
Image processing using the Mathematical morphology
EM Image Processing
Summarizing about the EM image processing here.
Montage and Panorama image
This is how to combine multiple images obtained by photographing the different regions (However, the set of image overlapping portion thereof ), to create an image of a large area.
CTF Collection
EM image has received the image modulation in principle. It is the image processing to correct the image modulation.
Alignment of 3D objects
It is a method for removing noise by averaging the three-dimensional image with each other.
Alignment of a series of images
It is a method for reconstructing a three-dimensional image by combining the position of the image between the serial sections.
3D Reconstruction
3D Reconstruction is a technique of reconstructing a three-dimensional image from a two-dimensional image.
Central Slice Theorem
Why can the internal structure be proved by the projected image? It is Central Slice Theorem that proves it.
Fourier method
Backprojection
SIRT
Electron Microscope
We here describe electron microscopy.
Electron gun
We here describe an electron source of electron microscope, a gun.
Lens
We here explain the mechanism of lens and optics, especially TEM (Transmission Electron Microscopy).
Contrast of TEM
We here explain what is contrast of TEM.
Contrast of SEM
We here explain what is contrast of SEM.
Contrast of STEM
We here explain what is contrast of STEM.
Electron cryo-microscopy
We here explain what is electron cryo-microscopy
FAQ of electron microscopy
We here answer the FAQ.
TIPS of electron microscopy
We here collect EM TIPS.
The future of Eos
The future of Eos (Loadmap) is shown here.
FAQ and TIPS
FAQ
We here plan to collenct FAQ(Frequenty asked question).
Eos TIPS
We here plan to collect TIPS in using Eos and processing/analyzing/intepreting images.
We here plan to collect useful TIPs around Eos. If you have some comments, please send me.
Why we have been developing Eos/PIONE ?
Comparing the date when Eos was born, 1996, many types of software for electron micrographs have been developed and used for more users and biologist. Nonetheless, we also ask ourselves the reason why we have been developing and maintenance Eos. We will note Why Eos by Yasunaga.
Eos User Group
We plan to create Eos User Group and discuss the current and the future of Eos on the sourceforge or facebook. Please access them.
About a symbol mark of Eos
Now we plan to make a symbol mark of Eos. If you have some ideas about Eos symbol, please send us yours.
If you want to know how to use mediawiki, please refer to User's Guid
Programming languages
Related workflow(PIONE)
Petri Net
Action description
Log file
Documentation tools
External link
- Eospedia.jp
- Eospedia.en
- Eos SourceForge
- Yasunaga Lab.
- Kyutech, Dept. of Bioscience and Bioinformatics
- Kyutech. School of Computer Science and Systems Engineering
- Kyushu Institute of Technology(Kyutech)