scipion-em-tomo 3.11.4

Plugin to use tomo within the Scipion framework

Base Scipion plugin for electron cryo-tomography and subtomogram averaging.

Protocols

• 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.

Latest plugin versions

If you want to check the latest version and release history go to CHANGES

Installing the plugin

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

Configuration variables

NAPARI_ENV_ACTIVATION (default = conda activate napari-0.4.19): Command to activate napari environment (used by other tomo plugins).

Buildbot status

Status devel version:

Status production version: