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eman2:e2tomosmall [2025/06/16 23:12] – created steveludtkeeman2:e2tomosmall [2025/06/18 10:56] (current) – steveludtke
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   * Make sure the workflow mode is set to "TOMO" not "SPR"   * Make sure the workflow mode is set to "TOMO" not "SPR"
  
-{{http://blake.bcm.edu/dl/EMAN2/e2pm.png|Project Manager|width="600"}}+{{https://blake.bcm.edu/dl/EMAN2/e2pm.png}}
  
   * **Raw Data -> Import tilt series**   * **Raw Data -> Import tilt series**
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   * It is critical that the filenames for your data not contain any spaces (replace with underscore) or periods (other than the final period used for the file extension).   * It is critical that the filenames for your data not contain any spaces (replace with underscore) or periods (other than the final period used for the file extension).
-  * <code>"%%__%%"</code> (double underscore) is also reserved for describing modified versions of the same file, and should not be used in your image filenames.+  * %%__%% (double underscore) is also reserved for describing modified versions of the same file, and should not be used in your image filenames.
   * If your tilt series isn't a single stack file, but is many individual images instead, you will need to use **Generate tiltseries** to build an image stack   * If your tilt series isn't a single stack file, but is many individual images instead, you will need to use **Generate tiltseries** to build an image stack
  
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   * Again, note that these files are not required by any downstream processing. If you have difficulty getting a particular tilt series to reconstruct, and the //patchtrack=2// option doesn't help, this may help debug the problem. However, if you do encounter problems, we would like to invite you to ask about it either publicly on the mailing list or privately to the developers.   * Again, note that these files are not required by any downstream processing. If you have difficulty getting a particular tilt series to reconstruct, and the //patchtrack=2// option doesn't help, this may help debug the problem. However, if you do encounter problems, we would like to invite you to ask about it either publicly on the mailing list or privately to the developers.
  
-{{http://blake.bcm.edu/dl/EMAN2/tomorecon.png|Tomogram reconstruction|width="600"}}+{{http://blake.bcm.edu/dl/EMAN2/tomorecon.png|Tomogram reconstruction}}
  
 When working with your own data: When working with your own data:
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 ===== Tomogram reconstruction evaluation ===== ===== Tomogram reconstruction evaluation =====
-{{http://blake.bcm.edu/dl/EMAN2/tomo_evaluation.png|Tomogram evaluation|width="600"}}+{{http://blake.bcm.edu/dl/EMAN2/tomo_evaluation.png}}
  
 **Analysis and visualization -> Evaluate tomograms** can be used to evaluate the quality of your tilt series alignments and tomogram reconstructions. This tool will show more information as you progress through the tutorial, but can be used already at this point to make various assessments of your tomograms. Note that some of this information may not be available if you had //notmp// checked during the reconstruction. **Analysis and visualization -> Evaluate tomograms** can be used to evaluate the quality of your tilt series alignments and tomogram reconstructions. This tool will show more information as you progress through the tutorial, but can be used already at this point to make various assessments of your tomograms. Note that some of this information may not be available if you had //notmp// checked during the reconstruction.
eman2/e2tomosmall.1750115557.txt.gz · Last modified: by steveludtke