Tutorial - Tomography streaming workflow
Table of Contents
Introduction
This tutorial guide you in a streaming tomography acquisition using Scipion. To achieve this goal, we will import the tilts as a movie in SPA, we will align those wit the align protocols of SPA, we will compose the tilt serie and as the last step we will generate the tomogram. All the steps running in streaming. A template to launch this workflow is available on the scipion-em-tomo plugin
Additional resources
Here you can find some valuable resources to complement the contents described in the tutorial:
Where to find the protocols?
Protocols needed to perform the workflow are available in the following plugins:
scipion-em
scipion-em-motioncor
scipion-em-tomo
scipion-em-aretomo
Workflow protocols
Importing and aligning movies as SPA
We will import al the tilts as we were in Single Particle, that way we will use the import movies protocol filling the form as common in SPA. Review the streaming parameters to be sure that the protocol works with the microscope condition (time to the next tilt (file timeout) and time to finish the acquisition (Timeout). You have to take into account that the workflow we propose admit several tiltseriee.
When the movies are being imported, we will continue alinging those movies. You can use the protocol to aling you consider, we propose on this workflow MotionCor, but you have to take into account that you can not use batches because could deform the image. Please set Number of patches as X=1 Y=1.
Composing tilt series
To generate a tilt serie we have released the Compose Tilt Serie protocol, available on scipion-em-tomo.
Some parameters must be filled before launch the workflow:
Input micrograph: Select as input the output of the align protocol
Path with the *.mdoc file for each TiltSerie: Select the directory that contain the mdoc files of each tiltSerie. The protocol will read each tilt fromn those mdoc files.
Streaming; Time for next tilt: elay (in seconds) until the next tilt is registered in the mdoc file. After timeout, if there is no new tilt, the tilt serie is considered as completed.Minimum time recomended 20 segs
Streaming; Time for next TiltSerie: Interval of time (in seconds) after which, if no new tilt serie is detected, the protocol will end. The default value is high (30 min) to avoid the protocol finishes during the acq of the microscope. You can also stop it from right click and press STOP_STREAMING.
Aligning tilts and generating tomograms
In order to generate a tomogram in streaming; in the time we have the tomogram of a tilt series to process the acquisition, we have enhanced the Aretomo protocol to manage the streaming process. None of the parameters must be filled in other than the usual ones available in the Aretomo protocol.
Summary
We have explained the workflow for managing a streaming acquisition. It requires only four protocols, two of them belong to the SPA field and the other two to the tomography field. The compose tilt series is a protocol designed ad-hoc for streaming tomography and the AreTomo protocol has been enhanced to allow streaming. In the future we plan to enable streaming tomography using other plugins such as IMOD.