- 1 Welcome to Eospedia
- 2 Beginner's Guid
- 3 Installation
- 4 Eos reference
- 5 Eos tutorial
- 5.1 How to set Eos environment
- 5.2 How to use commands of Eos
- 5.3 Image format on Eos
- 5.4 Simple image processing using Eos
- 5.5 CTF Correction
- 5.6 Single particle analysis
- 5.7 Electron Tomography
- 5.8 Notes
- 6 Developers' Guide of Eos
- 6.1 Eos System Architecture
- 6.2 For Eos System Developers
- 6.3 Eos System Commands
- 6.4 Eos development under Sourceforge
- 6.5 Development of small tools
- 6.6 How to create API
- 6.7 API list
- 6.8 Functional order of API
- 6.9 How to create integration commands
- 7 Image Processing and Image Analysis
- 7.1 General Image Processing
- 7.1.1 Simple Image Processing
- 7.1.2 Input of image and Lens
- 7.1.3 CTF, PSF and MTF
- 7.1.4 Sampling
- 7.1.5 Quantization
- 7.1.6 Noise reduction
- 7.1.7 Edge extraction
- 7.1.8 Binarization
- 7.1.9 Image processing using the Fourier space
- 7.1.10 Image processing using the Kernel of the Real space
- 7.1.11 Image processing using the Mathematical morphology
- 7.2 EM Image Processing
- 7.3 3D Reconstruction
- 7.1 General Image Processing
- 8 Electron Microscopy
- 9 The future of Eos
- 10 FAQ and TIPS
- 11 Why we have been developing Eos/PIONE ?
- 12 Eos User Group
- 13 About a symbol mark of Eos
- 14 Tools and Sites related to Eos
- 15 External link
- 16 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" on the facebook futher. We would like to spread using this.
Please contact Yasunaga for more information.
We here describe what is Eos.
We here describe commands of Eos by CUI.
We here describe how to integrate commands using make
We here show all of commands Eos supplies.
We here show functional order of Eos commands.
We here describe how to download Eos. We are currently developing a Eos at SourceForge.
We here describe how to install Eos.
We here describe how to install a new process flow control system, PIONE. PIONE has been developed on "github".
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.
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
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.
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
At first, we pick particles from electron micrographs. Here, the manual picking method is shown, although automatic methods are also proposed.
Next, we classify 2D-images following their shape and so average them per cluster to improve the ratio of signal to noise.
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.
Forth, we reconstruct 3D objects from 2D images, especially Backprojection.
FInally, we interpret 3D objects reconstructed from 2D images using visualization tools.
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.
Fist, we must correct CTF (Contrast Transfer Function) becuase the 2D images are taken with larger defocusing values.
Next, we align 2D images roughly using correlation between each image.
Third, we estimate the tilt-axis position and angles.
Fourth, we reconstruct 3D image from a set of tilt-series images.
We must pay attention of misleading blurring due to missing area, which is generated from the limitation of projection angles.
Last, we must perform segmentation of 3D objects to interpret them. Thus we must use computer-aided visualization tools.
Tomogram images of cryo-microscopy include a lot of noise, thus it is required the averaging of the particles have the same structure.
This tutorial pages were created with refer to the documents used single particle workshop on 2012/09/10-11.
Developers' Guide of Eos
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.
We here show functionl oder of API (Object-oriented libraries) supplied by Eos.
We describe how to develop integration commands.
We here show how to integrate commands using PIONE, which is a rule-based process definition and work under distributed computing system.
Here is the tutorial how to use PIONE.
Here, describe how to design process definition document by using PIONE.
Summarizing about the general image processing here.
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.
To convert analog images to digital images, it is important that discretize the space by decomposing. This step is called Sampling.
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).
In order to deal the image including a lot of noise, knowing well the nature of the noise is important.
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.
This is an important step in order to understand the shape of the object, but it is also a very difficult step.
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
Summarizing about the EM image processing here.
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.
EM image has received the image modulation in principle. It is the image processing to correct the image modulation.
It is a method for removing noise by averaging the three-dimensional image with each other.
It is a method for reconstructing a three-dimensional image by combining the position of the image between the serial sections.
3D Reconstruction is a technique of reconstructing a three-dimensional image from a two-dimensional image.
Why can the internal structure be proved by the projected image? It is Central Slice Theorem that proves it.
We here describe electron microscopy.
We here describe an electron source of electron microscope, a gun.
We here explain the mechanism of lens and optics, especially TEM (Transmission Electron Microscopy).
We here explain what is contrast of TEM.
We here explain what is contrast of SEM.
We here explain what is contrast of STEM.
We here explain what is electron cryo-microscopy
We here answer the FAQ.
We here collect EM TIPS.
The future of Eos (Loadmap) is shown here.
FAQ and TIPS
We here plan to collenct FAQ(Frequenty asked question).
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
- Eos SourceForge
- Yasunaga Lab.
- Kyutech, Dept. of Bioscience and Bioinformatics
- Kyutech. School of Computer Science and Systems Engineering
- Kyushu Institute of Technology(Kyutech)