Difference between revisions of "Getting started"
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== Getting help == | == Getting help == | ||
''Dynamo'' offers several ways of [[Getting help|getting help]] on specific subjects.... and of course, you can always [[https://groups.google.com/forum/#!forum/dynamo-for-cryo-electron-tomography contact our forum in Google Groups]] | ''Dynamo'' offers several ways of [[Getting help|getting help]] on specific subjects.... and of course, you can always [[https://groups.google.com/forum/#!forum/dynamo-for-cryo-electron-tomography contact our forum in Google Groups]] | ||
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| + | == Set of walkthroughs == | ||
| + | {| class="wikitable" style="margin:auto" | ||
| + | |+ Available walkthroughs sorted by topic | ||
| + | |- | ||
| + | ! scope="col" style="background-color:#4EDFD7" |Topic | ||
| + | ! scope="col" style="background-color:#4EDFD7" |Walkthrough | ||
| + | |- | ||
| + | ! scope="row" rowspan="4"| General | ||
| + | | style="background-color:#FFFFE5" | Starters guide | ||
| + | |- | ||
| + | | style="background-color:#FFFFE5" |Advanced starters guide | ||
| + | |- | ||
| + | | style="background-color:#FFFFE5" |Tips for management of tomographic data sets | ||
| + | |- | ||
| + | | style="background-color:#FFFFE5" |High resolution walkthrough with HIV1 | ||
| + | |- | ||
| + | ! scope="row" rowspan="4"| Models | ||
| + | | style="background-color:#ffffcc" | Dipole set models | ||
| + | |- | ||
| + | | style="background-color:#ffffcc" | Walkthrough on filament models | ||
| + | |- | ||
| + | | style="background-color:#ffffcc" | Walkthrough on vesicle models | ||
| + | |- | ||
| + | | style="background-color:#ffffcc" | Walkthrough on membrane models | ||
| + | |- | ||
| + | ! scope="row" rowspan="1" | PCA | ||
| + | | style="background-color:#FFFFE5" | Walkthrough on PCA through the command line | ||
| + | |- | ||
| + | ! scope="row" rowspan="2"| STA and MRA | ||
| + | | style="background-color:#ffffcc" | Walkthrough basic multireference | ||
| + | |- | ||
| + | | style="background-color:#ffffcc" | Walkthrough on adaptive bandpass filtering | ||
| + | |- | ||
| + | ! scope="row" rowspan="4"| Tilt series alignment | ||
| + | | style="background-color:#FFFFE5" | Walkthrough on manual marker clicking | ||
| + | |- | ||
| + | | style="background-color:#FFFFE5" | Walkthrough on GUI based tilt series alignment | ||
| + | |- | ||
| + | | style="background-color:#FFFFE5" | Walkthrough on command line based tilt series alignment | ||
| + | |- | ||
| + | | style="background-color:#FFFFE5" | Walkthrough on localized reconstruction | ||
| + | |- | ||
| + | ! scope="row" rowspan="4"| Template matching | ||
| + | | style="background-color:#ffffcc" | Walkthrough for template matching | ||
| + | |- | ||
| + | | style="background-color:#ffffcc" | Walkthrough for GUI-based template matching | ||
| + | |- | ||
| + | | style="background-color:#ffffcc" | Walkthrough for model-aware template matching | ||
| + | |- | ||
| + | | style="background-color:#ffffcc" | Programmatic GUI customization for template matching | ||
| + | |- | ||
| + | ! scope="row" rowspan="3"| Visualization | ||
| + | | style="background-color:#FFFFE5" | Walkthrough on placement of averages on table positions | ||
| + | |- | ||
| + | | style="background-color:#FFFFE5" | Walkthrough on creation of 3d scenes | ||
| + | |- | ||
| + | | style="background-color:#FFFFE5" | Walkthrough on hexagonal lattice coherence through neighborhood analysis | ||
| + | |- | ||
| + | ! scope="row" rowspan="1" | Others | ||
| + | | style="background-color:#ffffcc" | Integration with Warp and M | ||
| + | |- | ||
| + | |} | ||
Revision as of 15:40, 3 December 2024
The best way to learn Dynamoon your own is to follow the materials in one of our 2 day-workshops PSI Workshop 2023
Starters guide
Concerning the task of subtomogram averaging, you can get a plunge-freeze immersion in Dynamo for from scratch, by following the starters guide. This is a short hands-on complete walkthrough through the main functionalities in Dynamo: viewing and organizing tomograms, extracting particles, aligning, averaging and classifying subtomograms, and avoiding overfitting.
Getting help
Dynamo offers several ways of getting help on specific subjects.... and of course, you can always [contact our forum in Google Groups]
Set of walkthroughs
| Topic | Walkthrough |
|---|---|
| General | Starters guide |
| Advanced starters guide | |
| Tips for management of tomographic data sets | |
| High resolution walkthrough with HIV1 | |
| Models | Dipole set models |
| Walkthrough on filament models | |
| Walkthrough on vesicle models | |
| Walkthrough on membrane models | |
| PCA | Walkthrough on PCA through the command line |
| STA and MRA | Walkthrough basic multireference |
| Walkthrough on adaptive bandpass filtering | |
| Tilt series alignment | Walkthrough on manual marker clicking |
| Walkthrough on GUI based tilt series alignment | |
| Walkthrough on command line based tilt series alignment | |
| Walkthrough on localized reconstruction | |
| Template matching | Walkthrough for template matching |
| Walkthrough for GUI-based template matching | |
| Walkthrough for model-aware template matching | |
| Programmatic GUI customization for template matching | |
| Visualization | Walkthrough on placement of averages on table positions |
| Walkthrough on creation of 3d scenes | |
| Walkthrough on hexagonal lattice coherence through neighborhood analysis | |
| Others | Integration with Warp and M |
