Welcome to Eospedia
We started the new manual site of Eos for only few people at 05 Nov. 2010. We would like to summarize knowledges about Eos.
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.
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 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.
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.
- [Image Format|Image Format]]
- [Image format transform|Image format transform]]
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.
Nest, we align 2D images roughly using correlation between each image.
Third, we estimate the tilt-axis position and angles.
Forth, we reconstruct 3D image from a set of tilt-series images.
Problems of 3D reconstruction
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.
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.
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)