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Fetch metadata from EPU / SerialEM and launch on-the-fly pre-processing

Project description

# MDCatch ## Still in development, but you are welcome to try! A simple PyQt5 app to fetch metadata from EPU or SerialEM. It parses the first found EPU xml and SerialEM mdoc file associated with a data collection session. In case of SerialEM you need to enable saving mdoc file for each movie.

### Prerequisites / installation:
  • Python 3 and PyQt5. If you don’t have PyQt5 module in your system python3 then create a virtual environment: ` python3 -m venv venv source venv/bin/activate pip install PyQt5 `

  • Relion 3.1 or Scipion 3.0 sourced in your PATH (at the moment Scipion 3 is not ready!)

  • Preprocessing templates: Schedules folder for Relion, template.json for Scipion

  • Edit to adjust it to your settings

### Running
Simply python3 User only needs to provide:
  • path to EPU session folder or path to folder with SerialEM movies/mdoc files

  • particle size (A)

  • username

### Working principle The idea is to launch the app on a separate OTF machine as soon as EPU/SerialEM starts data collection and the first movie is acquired.

  1. check if username exists in the NIS database (ypmatch username passwd)

  2. find and parse the first xml/mdoc file, getting all acquisition metadata

  3. create a Relion/Scipion project folder username_microscope_date_time inside PROJECT_PATH (or inside Scipion default projects folder)

  4. create symlinks for movies, gain reference, defects file, MTF in the project folder

  5. modify existing Relion Schedules/Scipion templates then launch Relion/Scipion on-the-fly processing

### Screenshots

![Screenshot_20200103_182047]( ![Screenshot_20200103_182116](

### TODO
  • beam tilt is parsed but not used since we parse only a single xml/mdoc for the whole session

  • SerialEM conversions: gain ref dm4->mrc, defects SerialEM->Relion

  • K3 EPU 2.6.1 gain file is a rubbish tif, to be fixed by TFS

  • use GAIN_DICT from config

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