Difference between revisions of "Image format on Eos"
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| − | Image Handling on Eos | + | == Image Handling on Eos == |
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This section describes the image formats supported by Eos, and the method to convert the general image format into those ones. | This section describes the image formats supported by Eos, and the method to convert the general image format into those ones. | ||
| − | + | ||
| + | === Image format conversion === | ||
Data shot by electronic microscopes (hereinafter called EM) are different with each other. Since the MRC-type format is used on Eos, it is necessary to convert data into the MRC-type format. | Data shot by electronic microscopes (hereinafter called EM) are different with each other. Since the MRC-type format is used on Eos, it is necessary to convert data into the MRC-type format. | ||
• MRC2000-format | • MRC2000-format | ||
• MRC_file_format | • MRC_file_format | ||
• CCP4 File Format | • CCP4 File Format | ||
| − | + | ||
| + | === File conversion on Eos === | ||
1. Conversion from TIF to MRC (gray scale): tiff2mrc | 1. Conversion from TIF to MRC (gray scale): tiff2mrc | ||
Exercise: Convert the format of the supplied file, example-001.tif, into MRC. | Exercise: Convert the format of the supplied file, example-001.tif, into MRC. | ||
The sampling rate of this image’s pixels is 1.25A. Set RESOLUTION to 1.25. Name the output file example-001.mrc. | The sampling rate of this image’s pixels is 1.25A. Set RESOLUTION to 1.25. Name the output file example-001.mrc. | ||
| − | $ tiff2mrc -i example-001.tif -o example-001.mrc -R 1.25 | + | |
| + | $ tiff2mrc -i example-001.tif -o example-001.mrc -R 1.25 | ||
2. Conversion from MRC to TIF (gray scale): mrc2tiff | 2. Conversion from MRC to TIF (gray scale): mrc2tiff | ||
Exercise: Convert the format of the supplied file into TIFF. | Exercise: Convert the format of the supplied file into TIFF. | ||
Convert the MRC file which has been converted once above into a TIF file. Create an 8-bit TIF file with a name of example-001-8bit.tif. | Convert the MRC file which has been converted once above into a TIF file. Create an 8-bit TIF file with a name of example-001-8bit.tif. | ||
| − | $ mrc2tiff -i example-001.mrc -o example-001-8bit.tif | + | |
| + | $ mrc2tiff -i example-001.mrc -o example-001-8bit.tif | ||
3. Other tools | 3. Other tools | ||
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o dos2unix | o dos2unix | ||
| − | + | === MRC file formats on Eos === | |
Caution: Note that file formats are slightly different with each other even among the same MRC type. | Caution: Note that file formats are slightly different with each other even among the same MRC type. | ||
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1. Willy Wriggers: Situs, CCP4 and MRC 3D Density Map File Formats and Format Conventions report | 1. Willy Wriggers: Situs, CCP4 and MRC 3D Density Map File Formats and Format Conventions report | ||
| + | |||
When using Eos, be careful about the following: | When using Eos, be careful about the following: | ||
1. Length is usually handled with a sampling interval similar to that of voxel. Note that this is different from that of other formats. | 1. Length is usually handled with a sampling interval similar to that of voxel. Note that this is different from that of other formats. | ||
| + | |||
2. The CCP4-2000 (MRC2000) format has been supported gradually. Although the reading format is supported currently, the writing format is not supported perfectly yet. | 2. The CCP4-2000 (MRC2000) format has been supported gradually. Although the reading format is supported currently, the writing format is not supported perfectly yet. | ||
| + | |||
3. Some commands are not perfect. If there is something strange in the command behavior, confirm the symptom using mrcInfo, and Make settings using mrcInfoSet. | 3. Some commands are not perfect. If there is something strange in the command behavior, confirm the symptom using mrcInfo, and Make settings using mrcInfoSet. | ||
Latest revision as of 22:03, 10 June 2013
Contents
Image Handling on Eos
This section describes the image formats supported by Eos, and the method to convert the general image format into those ones.
Image format conversion
Data shot by electronic microscopes (hereinafter called EM) are different with each other. Since the MRC-type format is used on Eos, it is necessary to convert data into the MRC-type format. • MRC2000-format • MRC_file_format • CCP4 File Format
File conversion on Eos
1. Conversion from TIF to MRC (gray scale): tiff2mrc Exercise: Convert the format of the supplied file, example-001.tif, into MRC. The sampling rate of this image’s pixels is 1.25A. Set RESOLUTION to 1.25. Name the output file example-001.mrc.
$ tiff2mrc -i example-001.tif -o example-001.mrc -R 1.25
2. Conversion from MRC to TIF (gray scale): mrc2tiff Exercise: Convert the format of the supplied file into TIFF. Convert the MRC file which has been converted once above into a TIF file. Create an 8-bit TIF file with a name of example-001-8bit.tif.
$ mrc2tiff -i example-001.mrc -o example-001-8bit.tif
3. Other tools • Conversion from MRC o Conversion from MRC to GIF (gray scale): mrc2gif o Conversion from MRC to GIF (RGB-based coloring): mrcImageColoring o mrc2lattice o mrc2viff o mrc2fld o mrc2pov • Conversion to MRC o arra2mrc o emData2mrc o bin2mrc o ip2mrc o moi2mrc • Others o pdb2ucd o dos2unix
MRC file formats on Eos
Caution: Note that file formats are slightly different with each other even among the same MRC type.
1. Willy Wriggers: Situs, CCP4 and MRC 3D Density Map File Formats and Format Conventions report
When using Eos, be careful about the following: 1. Length is usually handled with a sampling interval similar to that of voxel. Note that this is different from that of other formats.
2. The CCP4-2000 (MRC2000) format has been supported gradually. Although the reading format is supported currently, the writing format is not supported perfectly yet.
3. Some commands are not perfect. If there is something strange in the command behavior, confirm the symptom using mrcInfo, and Make settings using mrcInfoSet.
