scipion-em-tomo 3.4.0

Plugin to use electron tomography software within the Scipion framework

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

This plugin is currently in BETA mode.

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.

• 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.

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-0.4.4): Command to activate napari environment (used by other tomo plugins).

Buildbot status

Status devel version:

Status production version: