Search results

Create the page "Alignment" on this wiki! See also the search results found.

• Depicting a cloud of observations on a tilt series
  ...> is the GUI that appears as exploration tool for tilt series when running alignment experiments. It can also be used independently of those workflows.
  2 KB (378 words) - 10:12, 8 July 2023
• Pasteur workshop 2017
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  2 KB (304 words) - 09:09, 19 July 2017
• Postprocessing plugins
  ...action that ''Dynamo'' will execute after each iteration during a project alignment.
  7 KB (1,043 words) - 17:07, 9 March 2017
• Principal component analysis
  ...icles. Thus, you need a [[data folder]] and a [[table]] that describes the alignment.
  3 KB (424 words) - 17:03, 28 March 2020
• Oblique slices in tomoslice
  :-Alignment of axes in orthogonal orientations
  3 KB (423 words) - 15:23, 27 April 2017
• Hints for purchase of computing resources
  ...aging, some steps in [[PCA]] analysis, manual management of models. Even [[alignment project]]s with modest number of particles can be reasonably executed on a ...tion, cropping particles, and any preprocessing related to the creation of alignment project. Once the project has been created (as a folder and an execution sc
  6 KB (966 words) - 13:34, 24 January 2022
• Walkthrough on adaptive bandpass filtering
  Masks are initiated to default values. This means spherical masks for alignment and classification masks, and full cubes for smoothing and fourier mask of Then select the number of available cores for alignment and averaging.
  10 KB (1,461 words) - 18:12, 27 November 2017
• Starters guide
  ...describes the basics including particle picking, initial model generation, alignment, averaging and classification or particles. ''Dynamo'' has a standalone to ...:StartersGuideParticlesUnaligned.png|thumb|center|400px| Particles without alignment (<tt>table</tt> is switched off).]]
  24 KB (3,775 words) - 14:39, 6 September 2021
• EMBO workshop 2018
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  3 KB (397 words) - 07:01, 5 September 2018
• Tips for management of tomographic data sets
  ...rder to make easy to keep track on the processing steps already performed (alignment, reconstruction), the location of the intermediate results, and their bindi In this example, we assume that you are using <tt>imod</tt> for tomographic alignment and reconstruction of each tilt series. The raw data is stored in a tree be
  8 KB (1,277 words) - 17:14, 16 May 2017
• Cropping unbinned particles after having worked with binned particles
  ...to ease computations, a binning order is passed to the [[Alignment project|alignment]] or classification project.
  8 KB (1,292 words) - 16:50, 6 February 2020
• Indicating the missing wedge
  ...will depend on the reconstruction program you used, and how it handled the alignment. Lets assume a <tt>ftype</tt> 1 (i.e., column 13 of table will be one). In
  3 KB (548 words) - 10:41, 3 April 2020
• Installation
  This shell is "activated" and can then be used to run [[alignment project]]s or to initiate an interactive session using the ''Dynamo'' [[Dyn
  3 KB (551 words) - 10:44, 26 March 2024
• Considerations for tomogram positioning in IMOD
  ...step and set the "Angle offset" and "Z shift" to zero. 2) Go to the "Fine Alignment" step and set the two values to zero too. Do ''not'' go back to the "Tomogr
  4 KB (646 words) - 13:34, 9 April 2019
• Walkthrough for lattices on vesicles (EMBO2023)
  ...n be used directly by ''Dynamo'' to operate an extraction and a subsequent alignment. ...s that are poorly defined still have a chance to get driven by a posterior alignment to the center of the box. If we initialize some variables:
  18 KB (3,069 words) - 12:21, 26 October 2023
• Walkthrough for lattices on vesicles
  ...n be used directly by ''Dynamo'' to operate an extraction and a subsequent alignment. ...s that are poorly defined still have a chance to get driven by a posterior alignment to the center of the box. If we initialize some variables:
  18 KB (3,099 words) - 12:19, 18 August 2021
• Walkthrough for lattices on vesicles (Copenhagen 2024)
  ...n be used directly by ''Dynamo'' to operate an extraction and a subsequent alignment. ...s that are poorly defined still have a chance to get driven by a posterior alignment to the center of the box. If we initialize some variables:
  18 KB (3,070 words) - 15:42, 22 January 2024
• Walkthrough on PCA through the command line (SciLifeLab 2023)
  ...than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a table that expreses the alignment
  13 KB (1,877 words) - 15:17, 26 October 2023
• San Diego Workshop 2018
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. ...[[adaptive bandpass filtering]], a way of conducting a ''golden standard'' alignment procedure . (~40 mins)
  13 KB (1,774 words) - 17:58, 26 January 2018
• Walkthrough on PCA through the command line (EMBO 2023)
  ...than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a table that expreses the alignment
  13 KB (1,933 words) - 12:36, 10 September 2023
• Walkthrough on PCA through the command line PSI 2023
  ...than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a table that expreses the alignment
  14 KB (1,967 words) - 17:42, 22 January 2024
• Walkthrough on PCA through the command line
  ...than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a table that expreses the alignment
  14 KB (1,969 words) - 21:58, 8 February 2021
• Walkthrough for template matching (SciLifeLab 2023)
  === Through manual alignment === ====Manual alignment of some particles ====
  25 KB (4,038 words) - 15:13, 25 October 2023
• Walkthrough for template matching (Göttingen 2024)
  === Through manual alignment === ====Manual alignment of some particles ====
  25 KB (4,038 words) - 11:14, 8 April 2024
• Walkthrough for template matching (EMBO2023)
  === Through manual alignment === ====Manual alignment of some particles ====
  26 KB (4,048 words) - 14:54, 8 September 2023
• Walkthrough for template matching
  === Through manual alignment === ====Manual alignment of some particles ====
  26 KB (4,071 words) - 13:53, 1 August 2023
• Walkthrough for template matching (PSI 2023)
  === Through manual alignment === ====Manual alignment of some particles ====
  26 KB (4,059 words) - 07:00, 17 August 2023
• Walkthrough on localized reconstruction
  ...b>sc</sub>'' and determined by the rotation axis implicitly defined by the alignment. Now, we could find the actual positions of the gold beads with an alignment project. We create a spherical template and mask:
  17 KB (2,770 words) - 14:44, 8 August 2022
• Computers Basel 2016
  #run your alignment by typing <tt>srun my_project.exe</tt>
  5 KB (815 words) - 14:20, 24 August 2017
• Computers Basel 2017
  # Create alignment project >> computational parameters >> system_gpu
  5 KB (843 words) - 10:23, 25 August 2017
• Practicals Birkbeck 2019
  [ 2 ] marked for alignment: 22 == Project for rotational alignment ==
  37 KB (5,792 words) - 18:30, 2 September 2019
• Framework for estimation of membrane thickness
  This framework is more useful in plastic sections. The premise is that an [[alignment project]] has been created to fix the position an orientation of a set of p
  5 KB (800 words) - 10:09, 9 May 2017
• Dynamo workshop 2017
  * Creation of alignment projects.
  4 KB (649 words) - 08:05, 27 August 2017
• Advanced starters guide (EMBO2021)
  [ 2 ] marked for alignment: 22 ...the ''standalone'' option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue box). See the [[EMBO_w
  46 KB (7,267 words) - 10:09, 13 September 2021
• Advanced starters guide (EMBO2023)
  [ 2 ] marked for alignment: 22 ...the ''standalone'' option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue box). See the [[EMBO_w
  46 KB (7,267 words) - 14:58, 8 September 2023
• Complete walkthrough on FHV virus (Copenhagen 2024)
  [ 2 ] marked for alignment: 22 ...the [[standalone]] option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue and green arrow) .
  46 KB (7,369 words) - 16:45, 22 January 2024
• Complete walkthrough on FHV virus (Göttingen 2024)
  [ 2 ] marked for alignment: 22 ...the [[standalone]] option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue and green arrow) .
  46 KB (7,369 words) - 11:20, 8 April 2024
• Complete walkthrough on FHV virus (SciLifeLab 2023)
  [ 2 ] marked for alignment: 22 ...the [[standalone]] option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue box) .
  46 KB (7,370 words) - 11:53, 20 October 2023
• Walkthrough on creation of 3d scenes
  * Proteins located in the tomogram, with the orientations provided during the alignment. we recover our table with locations '''and'' alignment parameters
  13 KB (2,062 words) - 10:46, 29 November 2017
• Advanced starters guide (PSI 2023)
  [ 2 ] marked for alignment: 22 ...the [[standalone]] option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue box) .
  46 KB (7,389 words) - 06:30, 16 August 2023
• Advanced starters guide
  [ 2 ] marked for alignment: 22 ...the [[standalone]] option. In both cases, select the number of cores for alignment (green box in the picture below) and averaging (blue box) .
  47 KB (7,440 words) - 16:36, 15 August 2023
• GPUs EMBO 2016
  #run your alignment by typing <tt>srun dynamo_execute_project my_project</tt>
  6 KB (1,053 words) - 07:58, 31 August 2016
• Construction of masks
  ...amo'' for several purposes: indicating the active part of the template for alignment, restricting the area of the aligned particles that will count for classifi
  6 KB (943 words) - 09:58, 14 September 2017
• Standalone
  ...ch "core" will be handled by a different openMP process. You can also run alignment projects in the GPU, in which case you also have to mark the set of [[GPU i
  7 KB (1,143 words) - 13:56, 4 May 2018
• Particle extraction
  ...the metadata. Data folder and table can directly be used for [[subtomogram alignment]]
  7 KB (1,221 words) - 14:46, 24 April 2018
• Walkthrough on PCA through the command line (Copenhagen 2024)
  ...than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a table that expresses the alignment.
  25 KB (3,619 words) - 08:57, 24 January 2024
• Walkthrough on PCA through the command line (Göttingen 2024)
  ...than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a table that expresses the alignment.
  25 KB (3,619 words) - 11:16, 8 April 2024
• HIV1 Walkthrough (PSI 2023)
  ...ion of the tilt series, contrast transfer function extraction, tilt series alignment, CTF correction, tomogram generation and modelling, subtomogram averaging a ...the tilts is crucial. This process will be done in this workshop after the alignment step.
  94 KB (15,184 words) - 12:28, 6 March 2024
• High Resolution workflow for HIV1 (SciLifeLab 2023)
  ...ion of the tilt series, contrast transfer function extraction, tilt series alignment, CTF correction, tomogram generation and modelling, subtomogram averaging a ...the tilts is crucial. This process will be done in this workshop after the alignment step.
  94 KB (15,184 words) - 12:26, 6 March 2024
• Compact HIV1 walkthrough (PSI 2023)
  ...ion of the tilt series, contrast transfer function extraction, tilt series alignment, CTF correction, tomogram generation and modelling, subtomogram averaging a ...the tilts is crucial. This process will be done in this workshop after the alignment step.
  95 KB (15,390 words) - 12:29, 6 March 2024
• HIV1 workshop
  ...ion of the tilt series, contrast transfer function extraction, tilt series alignment, CTF correction, tomogram generation and modelling, subtomogram averaging a ...e tilts is crucial. This process will be done in this walktrough after the alignment step.
  99 KB (15,898 words) - 12:27, 6 March 2024
• Delft Workshop 2017
  ...oductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  8 KB (1,246 words) - 11:51, 31 August 2017
• Walkthrough on hexagonal lattice coherence through neighborhood analysis
  We will use data from the initial gold standard alignment derived from five tomograms of immature HIV-1 virus-like particles.
  7 KB (962 words) - 14:16, 11 April 2024
• High resolution walkthrough with HIV1 (Göttingen 2024)
  ...ion of the tilt series, contrast transfer function extraction, tilt series alignment, CTF correction, tomogram generation and modelling, subtomogram averaging a ! Automatic tilt series alignment: alignment
  104 KB (16,757 words) - 11:17, 8 April 2024
• High resolution walkthrough with HIV1
  ...ion of the tilt series, contrast transfer function extraction, tilt series alignment, CTF correction, tomogram generation and modelling, subtomogram averaging a ! Automatic tilt series alignment: alignment
  104 KB (16,788 words) - 07:59, 13 May 2024

View (previous 100 | next 100) (20 | 50 | 100 | 250 | 500)