scipion-em-tomo 3.12.0

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 a Scipion sqlite file.

• import coordinates 3D : Protocol to import a set of coordinates 3D to the project.

• import subtomograms : Protocol to import a set of subtomograms to the project.

• import tomo CTFs : Protocol to import the CTF estimation of a set of tilt-series.

• Compose Tilt Series : Compose in streaming a set of tilt series based on sets of micrographs and mdoc files. Three time parameters are available for the streaming behaviour: time for next tilt, time for next micrograph and time for next tilt series.

• correct tilt offset : Correct the tilt angle offset of a tilt-series (particularly useful for lamellae) by adding a fixed offset to every tilt angle in the metadata.

• 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.

• exclude views filter : Filter a set of aligned tilt-series according to maximum allowed shift after alignment, accumulated dose range, tilt-angle range and minimum number of views.

• assign excluded views : Transfer excluded-view annotations (the _enabled state) from a source set of tilt-series to a target one. Tilt-series are matched by tsId and images by acquisition order, so it is robust to re-stacking.

• Tilt-series assign alignment : Assign the transformation matrices from an input set of tilt-series to a target one.

• tilt-series from tomograms : Get the tilt-series that correspond to a given set of tomograms. Useful for fiducial-less samples, to discard data at tomogram level and keep further processing with the matching tilt-series.

• misalign tilt-series : Introduce misalignment in the transformation matrix of a tilt-series (mainly for testing purposes).

• apply tomomasks to tomograms : Applies 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.

• 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.

• project coordinates : Project 3D coordinates into a set of landmarks.

• mask 3d coordinates : Filter a set of 3D coordinates using a segmentation (tomomask), keeping or excluding the coordinates that fall within a given segmentation label.

• meshes from tomo mask : Create meshes based on segmentations or voxel values (TomoMasks).

• 2D particles to subtomograms : Protocol to create a set of subtomograms from selected 2D particles.

• split even/odd tomos/subtomos : Protocol to split a set of tomograms or subtomograms into even/odd sets by element id.

• export 3D coordinates: Export 3D subtomogram coordinates to be used outside Scipion.

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: