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• Table convention
  The column convention used to define a table can be consulted by just typing <tt>dthelp</tt>, whi A set of euler angles in ZXZ convention.
  6 KB (809 words) - 09:22, 25 November 2019
• Table column convention
  {{DISPLAYTITLE:Table column convention}}
  5 KB (721 words) - 19:41, 8 March 2018
• Euler angles convention
  ''Dynamo'' uses a ZXZ convention to express the rotation in terms of Euler angles. A triplet of Euler angles
  2 KB (320 words) - 23:26, 4 August 2016
• Tilt angle convention
  ...portant that the tilt angles of your corresponding tilt series follow this convention. This ensures that within these different software packages the true handed To test if the angles in your tilt series follow the convention, the defocus on the left and right side of the tilt series can be estimated
  3 KB (502 words) - 13:42, 10 June 2020
• Angle of astigmatism convention
  ...IND4 output files. The output from ctffind4 can be converted into the IMOD convention with the function found in [https://github.com/C-CINA/TomographyTools Tomog
  985 bytes (158 words) - 15:21, 10 April 2019

Page text matches

• Angle of astigmatism convention
  ...IND4 output files. The output from ctffind4 can be converted into the IMOD convention with the function found in [https://github.com/C-CINA/TomographyTools Tomog
  985 bytes (158 words) - 15:21, 10 April 2019
• Tilt angle convention
  ...portant that the tilt angles of your corresponding tilt series follow this convention. This ensures that within these different software packages the true handed To test if the angles in your tilt series follow the convention, the defocus on the left and right side of the tilt series can be estimated
  3 KB (502 words) - 13:42, 10 June 2020
• Practical Suggestions for Tomographic Reconstruction
  === Naming convention and organizing data === ...commend to strictly follow a consistent file naming convention. A proposed convention is to use a number for the batch (a batch stands for one data acquisition s
  5 KB (871 words) - 15:59, 30 April 2019
• Symmetrization during alignment
  ...the center of the volume, defined by [[Volume center| the usual ''Dynamo'' convention]]
  591 bytes (90 words) - 13:50, 20 February 2018
• Volume center
  ...ons. For the formulas in this page, remember also that ''Dynamo'' uses the convention of counting pixels with the index 1, (not 0). The pixel "on the corner" wit For a volume of {{t|V}} NxNxN pixels, ''Dynamo'' considers by convention the pixel located at <tt> [N/2+1,N/2+1,N/2+1]</tt> as the central pixel of
  6 KB (936 words) - 11:01, 5 March 2018
• Refined table
  It follows the ''Dynamo'' [[Table convention|convention]] for tables. In particular, ''Dynamo'' should fill some columns in a ''re
  2 KB (304 words) - 11:15, 22 April 2016
• Subboxing
  ...</tt>,<tt>'ico_vertex'</tt>. The position of the symmetry axes is fixed by convention on each case. ...he C5 symmetry axes of the particle. As the orientation is defined by the convention, it is only necessary to provide the distance of a reference penton to the
  2 KB (374 words) - 17:54, 26 October 2017
• Prebinned tomograms
  ...be derived from the original tomogram following a specific [[#convention | convention]]. == Convention ==
  7 KB (1,183 words) - 16:19, 28 April 2017
• Table convention
  The column convention used to define a table can be consulted by just typing <tt>dthelp</tt>, whi A set of euler angles in ZXZ convention.
  6 KB (809 words) - 09:22, 25 November 2019
• Table
  ...r in mainly three scenarios. The [#Format convention in a table|formatting convention] is however always the same. ==Format convention in a table==
  8 KB (1,191 words) - 09:50, 1 June 2017
• Tips for management of tomographic data sets
  ...ng into a ''Dynamo'' [[catalogue]]. The idea is to keep and uniform naming convention that allows to comfortably locate the sought files and folders with simple ...ch will have its own folder under the <tt>data</tt> repository folder. The convention for the batch folder is a <tt>'b'</tt> character followed with an integer (
  8 KB (1,277 words) - 19:14, 16 May 2017
• Multireference alignment
  ...or pass a folder, where individuals files need to stick to a given naming convention. Each reference number is given by a three figure zero padded integer start ...the individual file names so as to follow the [[#Input format|appropriate convention]]
  4 KB (592 words) - 22:58, 6 June 2018
• Euler angles convention
  ''Dynamo'' uses a ZXZ convention to express the rotation in terms of Euler angles. A triplet of Euler angles
  2 KB (320 words) - 23:26, 4 August 2016
• File access through predefined profiles
  ...orking in one system, and you need to refer to file names expressed in the convention of the other system. ...to "relink" the tomograms (and linking elements in the models) to the mac convention. This works, but is rather tedious. Moreover, it also means that afterwards
  5 KB (870 words) - 16:07, 25 June 2018
• Angular search
  By convention, passing value 0 to <tt>inplane_range</tt> generates no ‘inplane’ rot
  3 KB (432 words) - 09:56, 2 May 2016
• Importing models
  ...es that you have computed externally (but parametrised with the ''Dynamo'' convention), you can also put them inside the model.
  3 KB (419 words) - 11:51, 12 March 2020
• Particle extraction
  ...ent experiments and merging the sets afterwards). ''Dynamo'' uses a single convention for the results of an extraction: This convention, explained [[Volume_center#While_particle_cropping| here]], ensures that p
  7 KB (1,221 words) - 16:46, 24 April 2018
• Binning tomograms
  The [[Catalogue]] uses an [[Viewing_tomograms#Prebinned_tomograms |specific convention]] that allows to store for each catalogued tomogram a binned version (or se
  3 KB (453 words) - 10:49, 20 May 2016
• DBox folder
  It defines several properties, principally the padding convention used for the tags of the particles and the size of the batch.
  4 KB (570 words) - 15:45, 12 October 2017
• Viewing tomograms
  ...requested by any browser, ''Dynamo'' will look if a file that follows this convention exists, and directly load it instead of computing the binning on the fly. ...can also bin the tomograms yourself. As long as they have the right naming convention described above, the Catalogue will find them.
  10 KB (1,652 words) - 11:49, 27 June 2018
• Data folder
  ...nfo}} checks if the contents of a folder are files with the correct naming convention, and reports their number and expected sidelength.
  4 KB (637 words) - 17:48, 30 September 2019
• Operations on volumes
  .../imod/doc/man/binvol.html command]. The binning factor follows a different convention. In Imod, the syntax:
  4 KB (666 words) - 11:45, 20 April 2017
• Table column convention
  {{DISPLAYTITLE:Table column convention}}
  5 KB (721 words) - 19:41, 8 March 2018
• Multilevel refinement
  By convention, passing equal values to ‘inplane_range’ and ‘inplane_sampling’ gen
  5 KB (786 words) - 10:35, 27 October 2017
• Alignment project
  ...a property (i.e., shifts, euler angles) according to a [[Table|predefined convention]]
  5 KB (793 words) - 09:41, 27 October 2017
• Daverage
  ...shifted, then rotated, following the alignment parameters in the table. By convention, positions 4:6 and 7:9 in a the <tt>i</tt>-th row in a table denote respec
  5 KB (792 words) - 15:09, 13 October 2017
• Matlab cell array
  ...ven string in their name. Thus, it is convenient to have a sensible naming convention while you create your models inside the tomograms, as it will facilitate ac
  6 KB (1,039 words) - 17:09, 23 February 2017
• Postprocessing plugins
  If you put your plugin as a system executable, the same naming convention will be used. You just need to skip the file extension <tt>.m</tt>.
  7 KB (1,043 words) - 19:07, 9 March 2017
• Pipelines for Workshop Heidelberg 2018
  ...that identifies a tilt series and creates an output with the right naming convention.
  7 KB (1,014 words) - 10:27, 22 August 2018
• Programmatic control of alignment and reconstruction workflows
  ...'-tasks'</tt>, followed by the a letter that identifies the task with this convention:
  12 KB (1,917 words) - 18:35, 10 July 2019
• Walkthrough on localized reconstruction
  Note that the default convention in <tt>dshow</tt> is to plot the rows of the matrix along the 'x' axis of t
  17 KB (2,770 words) - 11:57, 27 August 2018
• Advanced starters guide (EMBO2021)
  ...hat azimuthal rotations occur about an axis of possible symmetry, which by convention is located along z. There are several ways to achieve this. A simple one is
  46 KB (7,267 words) - 12:09, 13 September 2021
• Advanced starters guide
  ...hat azimuthal rotations occur about an axis of possible symmetry, which by convention is located along z. There are several ways to achieve this. A simple one is
  47 KB (7,432 words) - 18:41, 3 September 2021