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Tomography processing services

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Stephen Riggs edited this page Mar 14, 2025 · 1 revision

The tomography processing pipeline consists of:

  • Motion correction
  • CTF estimation
  • Tomogram alignment and reconstruction
  • Tomogram denoising using Topaz
  • Segmentation using membrain-seg

Requirements

The following executables need to be accessible by the processing services:

  • MotionCor2
  • ctffind4
  • Imod (specifically newstack and rotatevol)
  • AreTomo2

Workflow

The following processing services need to be run: ProcessRecipe, MotionCorr, CTFFind, TomoAlign, Denoise, MembrainSeg

Optionally, Images and NodeCreator services can be run to create thumbnail images and write Relion 5 star files. If an ispyb database is available the results can be inserted into that with the EMISPyB service.

tomo_outline

All the services are started using:

$ cryoemservices.service -s <service> -c config_file.yaml

MotionCorr, TomoAlign, Denoise and MembrainSeg run programs requiring a GPU.

The processing services receive messages from and send feedback to RabbitMQ. The preprocessing (motion correction and ctffind) run on individual tilt image stacks, while the tomogram alignment and reconstruction needs lists of motion corrected tilts. These can be coordinated using Murfey, which requests the preprocessing, and handles the feedback from this to decide when to run alignment.

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