Base Scipion plugin for electron cryo-tomography and subtomogram averaging.
- import tilt-series: Protocol to import tilt series.
- import tilt-series movies: Protocol to import tilt series movies.
- import tomograms : Protocol to import a set of tomograms to the project.
- import tomomasks (segmentations): Protocol to import a set of tomomasks (segmentations) to the project.
- import 3D coordinates from scipion : Protocol to import a set of 3d coordinates from Scipion sqlite file.
- import set of coordinates 3D : Protocol to import a set of coordinates 3D to the project.
- import subtomograms : Protocol to import a set of tomograms to the project.
- 2D particles to subtomograms : Protocol to create a set of subtomograms from a selected 2D particles.
- 2d coordinates to 3d coordinates : Turns 2d coordinates into set of 3d coordinates. Works in coordination with 'tomograms to micrographs' protocol.
- Compose Tilt Serie : Compose in streaming a set of tilt series based on a sets of micrographs and mdoc files. Three time parameters are abailable for the streaming behaviour: Time for next tilt, Time for next micrograph and Time for next Tilt Serie
- Tilt-series assign alignment : Assign the transformation matrices from an input set of tilt-series to a target one.
- Tilt-series consensus alignment : Perform a consensus of a set of alignments for the same tilt series. Returns the average alignment matrix of the consensus alignments and its standard deviation of shift and angle.
- Tilt-series convert coords3D : Scipion protocol to convert a set of tilt-series coordinates 3d to a set of coordinates 3d associated to a set of tomograms.
- assign alignment : Assign the alignment stored in a set of Subtomograms/Coordinates3D to another set. Both sets should have same pixel size (A/px). The Subtomograms/Coordinates3D with the alignment can also be a subset of a bigger set.
- assign tomograms to tomo masks (segmentations) : This protocol assign tomograms to tomomasks (segmentations).
- assign tomos to subtomos : This protocol assign tomograms to subtomograms that have been imported before without tomograms. Subtomograms should contain the name of the original tomogram in their own file name.
- average tilt-series movies : Simple protocol to average TiltSeries movies as basic motion correction. It is used mainly for testing purposes.
- consensus classes subtomo : Compare several SetOfClassesSubTomograms. Return the intersection of the input classes.
- ctf validate : Validate a set of CTF tomo series and separate into two sets (good and bad tomo series )
- extract 3D coordinates : Extract the coordinates information from a set of subtomograms. This protocol is useful when we want to re-extract the subtomograms (maybe resulting from classification) with the original dimensions. It can be also handy to visualize the resulting subtomograms in their location on the tomograms.
- export 3D coordinates: Export 3D subtomogram coordinates to be used outside Scipion.
- split even/odd tomos/subtomos : Protocol to split set of tomograms or subtomograms in even/odd sets by element id.
- tomograms to micrographs : Turns tomograms into set of micrographs to apply SPA picking methods.
- apply tomomasks to tomograms : Aplies a set of masks to a given set of tomograms. Some operations can be applied to the mask: invert, dilate and apply a gaussian filter.
- invert tilt angles : Inverts the physical handedness of the introduced tilt-series by inverting the tilt angles in the metadata associated to each tilt-series.
If you want to check the latest version and release history go to CHANGES
In order to install the plugin follow these instructions:
scipion installp -p scipion-em-tomo
or through the plugin manager by launching Scipion and following Configuration >> Plugins
To install in development mode
Clone or download the plugin repository
git clone -b devel https://github.com/scipion-em/scipion-em-tomo.git
Install the plugin in developer mode.
scipion installp -p local/path/to/scipion-em-tomo --devel
NAPARI_ENV_ACTIVATION (default = conda activate napari-0.4.19): Command to activate napari environment (used by other tomo plugins).
Status devel version:
Status production version:
