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• Particle picking
  ...s (and possibly) euler angles that roughly correspond to the presence of a particle. * Particle picking
  2 KB (340 words) - 13:31, 23 February 2017
• Particle extraction
  Particle extraction is the process of using a set of positions (and possibly orienta ==Results of a particle extraction==
  7 KB (1,221 words) - 16:46, 24 April 2018
• Particle File List
  The Particle File List is a [[Generic data containers | generic data container]] that ca ...alue of <tt>tag</tt> property inside the object, '''not''' by the name of particle file (unlike in a classic Dynamo folder).
  7 KB (1,151 words) - 13:01, 30 November 2020
• Particle swapping in multireference projects
  ...th ''all'' the particles. The score of each particle is computed, and each particle is assigned (at the end of each iteration) to a different template. The end ...be assigned to different channels.... they'll "swap", until a point where particle membership estabilizes from iteration to iteration. In this point, the part
  1 KB (151 words) - 10:42, 15 April 2016

Page text matches

• Eigencomponents
  ...'eigencomponents'' of a particle the coefficients of the expansion of this particle on the basis of the computed eigenvolumes. ...nts a particle. In that row, the entry number 41 is the projection of this particle along eigenvolume number 1, and so on.
  428 bytes (63 words) - 15:50, 26 May 2016
• Fourier acceleration
  ...emplate, the normalized cross correlation of shifted template and the data particle is computed. This operation is formally known as the ''correlation'' of two ...yway, (in order to apply a bandpass, or to impose the missing wedge of the particle onto the template).
  2 KB (242 words) - 10:38, 18 April 2016
• Volume table index file
  When produced by ''Dynamo'', during [[particle extraction]], a volume table index file is a text file stored inside a [[da ...ser can produce their own files with the same structure for a customized [[particle extraction]] using {{docfunction|dynamo_table_crop|dtcrop}}
  617 bytes (97 words) - 15:38, 27 April 2016
• Particle swapping in multireference projects
  ...th ''all'' the particles. The score of each particle is computed, and each particle is assigned (at the end of each iteration) to a different template. The end ...be assigned to different channels.... they'll "swap", until a point where particle membership estabilizes from iteration to iteration. In this point, the part
  1 KB (151 words) - 10:42, 15 April 2016
• Particle picking
  ...s (and possibly) euler angles that roughly correspond to the presence of a particle. * Particle picking
  2 KB (340 words) - 13:31, 23 February 2017
• Euler angles convention
  ...aligned with the z direction. The action of the triplet of angles of this particle would be like this. #;The particle rotates clockwise about its z axis.
  2 KB (320 words) - 23:26, 4 August 2016
• Pdf tutorials
  ==Catalogues and particle picking== * Introduction to particle picking {{pdftutorial|click_particles|link}}.
  2 KB (208 words) - 13:19, 29 April 2016
• Why is GPU not available for classification?
  ...ding part is the construction of the [[cross correlation matrix]]. Here, a particle read from the disk just experiences a rotation, a fourier filtering and a d
  715 bytes (111 words) - 13:10, 19 April 2016
• Alignment mask
  ...o define the part of the template cube that will actually be used to align particle. The rotated and shifted template is compared to the data particle only inside this moving region.
  3 KB (431 words) - 14:29, 15 April 2016
• Fourier mask on template
  ...of the tomogram (which is indicated through the [[table]] on a particle by particle way). ...e template fourier mask as ''unknown'' when comparing the template and the particle (which will have its own map of known and unknown Fourier coefficients).
  1 KB (204 words) - 10:25, 6 July 2017
• Border alignment artifact
  When rotating a cube, the cube representing the rotated particle will have some areas where there is no information. As a consequence, a rotated particle appears as showing an "edge". Most ''Dynamo'' programs rotate the volume in
  760 bytes (102 words) - 09:33, 13 October 2017
• Fourier compensation during averaging
  ...single tomogram and thus share the same missing wedge, after rotation each particle will cover a different area of the Fourier space. As the particles have dif As each particle has a different missing wedge, the resulting addition is not "well compensa
  4 KB (582 words) - 12:06, 21 November 2017
• Subboxing
  ...subboxed table can be used to recrop a new [[data folder]], in which each particle file will contain a subunit. Each subboxed particle file will contain a subunit. The density map particle itself is stored (as always in ''Dynamo'') without any rotation: the fact
  2 KB (374 words) - 17:54, 26 October 2017
• Generic data containers
  * [[Particle File List]]s.
  210 bytes (34 words) - 17:49, 30 September 2019
• Video tutorials
  ==Particle picking ==
  1 KB (226 words) - 10:24, 1 June 2016
• Indicating the missing wedge
  ...ed in columns 13 to 19 of a table (remember that a row represents a single particle). ...s created during particle cropping will express the missing wedge for each particle in the corresponding columns.
  3 KB (548 words) - 12:41, 3 April 2020
• Data folder
  ...rams. Other formats are [[DBox folder | dBoxes]] or [[Particle List File | Particle List File]] ...intuitive way of organizing your data is just to create one file for each particle inside the data folder. For instance, if you have 150 subtomograms, you ca
  4 KB (637 words) - 17:48, 30 September 2019
• Memory/speed balance during ccmatrix computation
  ...hand, if ''M'' is too big (in the extreme case, ''M''=''N'', so that each particle gets read from disk and aligned just once), then you might need a huge amou
  2 KB (316 words) - 11:14, 19 April 2016
• Dcm GUI
  ==Particle cropping==
  2 KB (285 words) - 17:42, 21 March 2016
• Volume center
  === While particle cropping === ==== Cropping positions of particle centers ====
  6 KB (936 words) - 11:01, 5 March 2018
• Angular search
  ...plate is rotated several times, and each rotated copy is compared with the particle. ...rticles. The last one, <tt>old_angles</tt> is obviously different for each particle, and in runtime is read from the table (provided by the user or [[Refined t
  3 KB (432 words) - 09:56, 2 May 2016
• Table column convention
  ...e significance of each column in a [[table]]. Each row represents a single particle. Identifies the particle number, so that each particle in the [[data folder]] indexed by the table is identified.
  5 KB (721 words) - 19:41, 8 March 2018
• Workshop exercises
  * Based on the particle tag (i.e., extract a subtable indexing only particles in a range of tags). == Particle extraction==
  4 KB (698 words) - 10:30, 1 September 2016
• Principal component analysis
  ...ticle can be represented by the contributions of each "eigenvolume" to the particle, i.e., by a set of "eigencomponents", normally in a number no much higher t ...(although much less intensive than the computation of the ccmatrix). Each particle is compared to each eigenvolume.
  3 KB (424 words) - 19:03, 28 March 2020
• Refined table
  * columns 3 (marks if the particle was actually used for the average produced at the iteration) * column 10 10 (the cross correlation coefficient computed for the alignment particle)
  2 KB (304 words) - 11:15, 22 April 2016
• Spectral averages in PCA
  ...is frequently frustrating not to detect a clear trend in the histograms of particle [[eigencomponents]]. Nevertheless, you might still manage to identify salie ...ting each eigenvolume separately, computing a weight as the average of all particle eigencomponents for that eigenvolume together. Then all the so weighted eig
  2 KB (351 words) - 15:53, 26 May 2016
• Framework for estimation of membrane thickness
  ...to get an estimation on the distance between the membrane layers on each ''particle''. This task can be performed through a [[multireference analysis]], but it gets the particle with tag 12 as a variable <tt>p</tt> in the workspace. You can also read al
  5 KB (800 words) - 12:09, 9 May 2017
• Multireference alignment
  In a multireference alignment [MRA] project, each particle will be aligned against R different templates. ...particles, each particle will be aligned against all the R references. The particle will produce R different cross-correlation scores and R different sets of a
  4 KB (592 words) - 22:58, 6 June 2018
• Multireference Analysis
  ...st match a given reference are used in the averaging step. Informally, the particle ''chooses'' which class it belongs to.
  1 KB (215 words) - 10:37, 19 August 2020
• Helical symmetry
  ==Symmetrizing a particle== Symmetrizing a helical particle can be done with the usual tool {{t|dsym}}:
  3 KB (429 words) - 15:32, 1 June 2016
• Table convention
  1 : tag tag of particle file in data folder 2 : aligned value 1: marks the particle for alignment
  6 KB (809 words) - 09:22, 25 November 2019
• Particle extraction
  Particle extraction is the process of using a set of positions (and possibly orienta ==Results of a particle extraction==
  7 KB (1,221 words) - 16:46, 24 April 2018
• Seed oversampling
  ...the physical size of the particle and the sidelength that you ask for the particle cropping. ...e with the highest correlation will be kept, and any other particle in the particle radius will be eliminated.
  4 KB (683 words) - 13:51, 3 February 2017
• Shift limits
  ...the ''way'' the limits are imposed (i.e., from which position in the data particle) is controled by <tt> area_search_modus</tt> or <tt>limm</tt>: *2: shifts limits are imposed from the putative position of the particle as computed by a previous iteration.
  1 KB (245 words) - 10:13, 26 October 2016
• Particle File List
  The Particle File List is a [[Generic data containers | generic data container]] that ca ...alue of <tt>tag</tt> property inside the object, '''not''' by the name of particle file (unlike in a classic Dynamo folder).
  7 KB (1,151 words) - 13:01, 30 November 2020
• Subtomogram alignment
  Aligning subtomograms is the process of computing for each available particle the set of shifts and angles that will bring them to a common reference.
  674 bytes (101 words) - 19:02, 29 April 2016
• Daverage
  ...ion (first rotation, then shifting). The shifts and angles that bring the particle to match the template are the ones that parametrize the inverse transform: and the operation that creates the aligned particle can be written as :
  5 KB (792 words) - 15:09, 13 October 2017
• DBox folder
  The ''dBox'' folder is an alternate way to store particle files. When you have, say, 100K files, it is a bad idea to put all of the % file of particle in original folder
  4 KB (570 words) - 15:45, 12 October 2017
• Getting started
  ...': [[Viewing tomograms|viewing]] and [[Catalogue|organizing]] tomograms, [[Particle extraction|extracting particles]], [[Subtomogram alignment|aligning]], aver
  943 bytes (119 words) - 11:08, 26 February 2021
• Cropping table
  A ''cropping table'' is a regular table used in the context of [[particle extraction]]. ''Dynamo'' uses internally tables to execute all particle extraction operations through the [[catalogue]]. If you want to generate [[
  5 KB (787 words) - 14:49, 23 May 2018
• Multilevel refinement
  ...project runtim. The last one, ‘old_angles’ is obviously different for each particle, and in runtime is read from the table (provided by the user or generated b ...ing the full cross correlation matrix between the rotated template and the particle. Then, a shift limiting is applied onto the matrix, and the maximal cc insi
  5 KB (786 words) - 10:35, 27 October 2017
• Table
  ...ch we call a ''tag'') that identifies a particle. In the data folder, this particle is identified by the name of the file that contains it, i.e. ...n the data folder <tt>myData</tt>. A table will be able to operate on this particle if it has a row whose first column is the integer 3.
  8 KB (1,191 words) - 09:50, 1 June 2017
• Jobs
  * Proficiency in single particle cryo-EM image processing and 3D reconstruction. * Process single particle cryo-EM data including handling raw data, interpretation, 3D reconstruction
  3 KB (389 words) - 18:17, 22 December 2020
• Adaptive bandpass filtering
  * doesn't [[Particle swapping in multireference projects | swap particles]] between references, ...nce channels, but without [[Particle swapping in multireference projects | particle swapping]]
  4 KB (666 words) - 09:10, 28 November 2017
• Integration with Warp and M
  * multi-particle refinement * Run multi-particle refinements in M
  6 KB (992 words) - 13:47, 19 August 2020
• GPU
  It also depends on the particle size and on the number of angles scanned per particle (higher number will yield higher speed up factors, i.e., the more intensive ...reference alignment: the cc of many rotations of the template against the particle can be computed inside the GPU without any transfer of data into the CPU or
  5 KB (902 words) - 08:44, 2 September 2016
• Tomogram-table map file
  Such files are created automatically during [[particle extraction]] through the catalogue. In the [[data folder]] created by ''D
  1 KB (192 words) - 12:23, 26 April 2017
• Walkthrough basic multireference
  ...The reason is that what we just ran was a multireference project ''without particle swapping'', i.ie., the particles where aligned separately and were never al
  1 KB (221 words) - 13:06, 16 August 2016
• Dipole set models
  ...he <tt>west</tt> to <tt>center</tt> axis will define the ''x'' axis of the particle. Sometimes it is useful to be able to directly collect the orientation of the particle from a simple interaction with the tomogram (obviously only for particles w
  7 KB (1,266 words) - 18:20, 24 February 2017
• Linking surfaces into point models
  ...normal, and formats it to provide the three euler angles needed to crop a particle.
  2 KB (266 words) - 15:25, 14 July 2017
• Starters guide (EMBO2021)
  =Manual particle picking and ''Dynamo'' catalogues= ...can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the
  15 KB (2,422 words) - 16:17, 13 September 2021
• Starters guide (workshop version)
  =Manual particle picking and ''Dynamo'' catalogues= ...can navigate up and down the tomogram, place the mouse on the center of a particle and press the [c] key on your keyboard to add a new model point. (Note the
  15 KB (2,427 words) - 19:27, 3 September 2021
• Dynamo Workshop CIC bioGUNE 2020
  ...t and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement * Manual and automated particle picking in different geometries (filaments, membranes, isolated particles..
  4 KB (570 words) - 18:01, 11 August 2020
• Operations on volumes
  ...hen processing 3d data, both for small volumes (as templates, averages and particle) or tomograms. ''Dynamo'' and Matlab itself provide several commands. ...ther instances of ''Dynamo'' (normally under the name {{t|actions}} or {{t|particle actions}}) when volumetric transformations are operated on the fly. For ins
  4 KB (666 words) - 11:45, 20 April 2017
• Walkthrough on PCA through the command line
  ...128 particles where 64 of the, are slightly smaller than the other 64. The particle subtomogram are randomly oriented, but the alignment parameters are known. * a mask that indicates the area of each alignment particle that will be taken into account during the classification procedure.
  14 KB (1,969 words) - 23:58, 8 February 2021
• Averaging of subtomograms
  ...s provided and the ''norm'' flag is tuned to 1 (as it is by default), each particle will be normalized to have zero mean and standard deviation 1 inside this m *<tt>'implicitRotationMasking'</tt>. If tuned to 1, the contribution of the particle outside an interior sphere will be discarded to minimize [[Border alignment
  5 KB (818 words) - 18:09, 6 December 2017
• Basel Workshop 2019
  ...t and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement * Manual and automated particle picking in different geometries (filaments, membranes, isolated particles..
  4 KB (662 words) - 12:07, 12 October 2021
• Basel Dynamo Workshop 2018
  ...t and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement * Manual and automated particle picking in different geometries (filaments, membranes, isolated particles..
  5 KB (673 words) - 15:26, 27 August 2018
• Model
  [[Category:Particle picking]] ...l application of a model is in [[Particle picking|particle picking]] and [[Particle extraction|extraction]].
  10 KB (1,574 words) - 11:00, 2 May 2017
• Fourier Shell Correlation
  ...he zero-th component of the Fourier transform (i.e, the total intensity of particle ''a'' in direct space). The FSC of the central Fourier model of two volumes
  2 KB (357 words) - 08:40, 27 April 2016
• Alignment project
  ...ng the particles cropped out of the tomograms. The easiest format to store particle data is the [[Data folder |data folder]]. ...he metadata on the particles. A table is basically a matrix representing a particle at each row, each column representing a property (i.e., shifts, euler angl
  5 KB (793 words) - 09:41, 27 October 2017
• Practical Suggestions for Tomographic Reconstruction
  ...reconstructed tomograms to facilitate the particle detection and the first particle alignment iterations. SIRT tomograms have usually higher contrast but a low
  5 KB (871 words) - 15:59, 30 April 2019
• Dynamo workshop 2017
  ...mpassing all stages of the pipeline: tomogram visualization and archiving, particle picking, averaging, refinement and classification. No previous experience i * Particle picking in different geometries: filaments, membranes, vesicles.
  4 KB (649 words) - 10:05, 27 August 2017
• Prato Workshop 2018
  ===Particle picking===
  7 KB (984 words) - 14:31, 12 April 2018
• Walkthrough on filament models
  ...am extraction (cropping). Click on ''create final positions and angles for particle cropping''. Ignore the angles, as they are not part of this model. Visualiz ...o 20 (see orange box). Click again ''create final positions and angles for particle cropping'' to update the information and visualize the new crop points:
  6 KB (1,042 words) - 16:52, 12 August 2021
• Starters guide
  ...from cryo electron tomograms. This document describes the basics including particle picking, initial model generation, alignment, averaging and classification ==Particle picking and ''Dynamo'' catalogues==
  24 KB (3,775 words) - 16:39, 6 September 2021
• Computing environments
  ...and read into memory one at a time for ''each process''. After reading one particle (a time expensive operation), the memory of the process will keep in a give
  2 KB (397 words) - 09:43, 29 April 2016
• Getting a Structure from Multiple Tomograms of HIV Capsids
  ...epared a set of 6 tomograms, each containing one Immature HIV-1 virus like particle(VLP) with a layer formed by a lattice of capsid proteins. The capsid protei
  3 KB (489 words) - 15:16, 27 August 2020
• Programmatic reconstruction of tomograms
  ...structions with a sharper contrast, which are useful for visualization and particle picking.
  3 KB (496 words) - 11:10, 3 July 2018
• ''Dynamo''workshop at the New York Structural Biology Center 2016
  ...mpassing all stages of the pipeline: tomogram visualization and archiving, particle picking, averaging, refinement and classification. No previous experience w
  3 KB (436 words) - 16:09, 9 December 2016
• Walkthrough on command line based tilt series alignment
  To manually define the particle coordinates, we first open a new model of type <tt>general</tt>: Right click on the (x,y) position of a particle opens two small windows showing the x-z and y-z planes:
  12 KB (1,823 words) - 12:15, 11 August 2021
• Walkthrough for template matching
  ...ange of the depicted particles moving the slider bar. When you do so, each particle will appear in the scene as a single red box. or the number of slices that are projected into the depicted image for each particle.
  25 KB (3,943 words) - 14:11, 18 August 2021
• Walkthrough for lattices on vesicles
  ...us ask ''Dynamo'' to operate the table merging by itself, and renaming the particle tags. With the order: we concatenate the tables inside the cell array <tt>tv</tt> and set the particle tags (in column 1) to be named from 1 to the maximal number of particles to
  18 KB (3,099 words) - 14:19, 18 August 2021
• Walkthrough on adaptive bandpass filtering
  ...ise 0.2 </tt> adds gaussian noise of the given amplitude to each synthetic particle * We don't let the parameters drive away from the center of the particle (limit modus 1) more that 4 pixels.
  10 KB (1,461 words) - 20:12, 27 November 2017
• EMBO workshop 2020
  ...-series alignment and particle picking and plug the results into M's multi-particle refinement
  9 KB (1,391 words) - 16:19, 25 August 2020
• Hints for improving a refinement
  where <tt>myTable</tt> is probably a subtable of your all-particle table... If you have a global table embracing many tomograms, with many geo
  5 KB (720 words) - 15:53, 19 May 2016
• Catalogue
  Keeping a ''catalogue'' is not necessary for [[particle extraction|cropping particles]] out of your tomograms. The tools associated
  5 KB (855 words) - 22:28, 14 August 2017
• Volume list file
  Volume list files are useful to [[particle extraction|extract particles]] from multiple tomograms into the same [[data
  6 KB (906 words) - 16:24, 10 April 2020
• Filament model
  The manually introduced points need to be converted into particle points.
  6 KB (944 words) - 16:29, 15 August 2016
• Hints for purchase of computing resources
  ...rations frequently needed in ''Dynamo'' that benefit from parallelization: particle cropping, averaging, some steps in [[PCA]] analysis, manual management of m
  6 KB (966 words) - 15:34, 24 January 2022
• Walkthrough on membrane models
  Press the button ''create final positions and angles for particle cropping'' and visualize the crop positions:
  7 KB (1,174 words) - 10:23, 13 August 2021
• Advanced starters guide (EMBO2021)
  == Annotation of particle positions == ...ate the table variable <tt>t</tt>, it is just a matrix with a row for each particle, and a summary of the information coded inside can be created through:
  46 KB (7,267 words) - 12:09, 13 September 2021
• Practicals Birkbeck 2019
  == Annotation of particle positions == ...ate the table variable <tt>t</tt>, it is just a matrix with a row for each particle, and a summary of the information coded inside can be created through:
  37 KB (5,792 words) - 20:30, 2 September 2019
• Cropping unbinned particles after having worked with binned particles
  * Keeping one [[catalogue]] to [[Particle extraction|crop particles]] in full resolution.
  8 KB (1,292 words) - 18:50, 6 February 2020
• Advanced starters guide
  == Annotation of particle positions == ...ate the table variable <tt>t</tt>, it is just a matrix with a row for each particle, and a summary of the information coded inside can be created through:
  47 KB (7,432 words) - 18:41, 3 September 2021
• Viewing tomograms
  ...tructed with SART (typically providing a nice contrast) for depiction and particle clicking.
  10 KB (1,652 words) - 11:49, 27 June 2018
• Getting a Structure from Multiple Tomograms of HIV Capsids (walkthrough)
  ...epared a set of 6 tomograms, each containing one Immature HIV-1 virus like particle (VLP) with a layer formed by a lattice of capsid proteins. The capsid prote A quick look at the newly aligned average should show a nicely centered particle with the symmetry axis aligned to the Z axis.
  22 KB (3,572 words) - 14:13, 18 August 2021
• San Diego Workshop 2018
  | ''Automated particle picking through template matching''
  13 KB (1,774 words) - 19:58, 26 January 2018