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 config.py to adjust it to your settings
- ### Running
- Simply python3 run.py. 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.
check if username exists in the NIS database (ypmatch username passwd)
find and parse the first xml/mdoc file, getting all acquisition metadata
create a Relion/Scipion project folder username_microscope_date_time inside PROJECT_PATH (or inside Scipion default projects folder)
create symlinks for movies, gain reference, defects file, MTF in the project folder
modify existing Relion Schedules/Scipion templates then launch Relion/Scipion on-the-fly processing
### Screenshots
![Screenshot_20200103_182047](https://user-images.githubusercontent.com/6952870/71741099-e2c6d200-2e55-11ea-9c98-66a14dc8cb2e.png) ![Screenshot_20200103_182116](https://user-images.githubusercontent.com/6952870/71741103-e5292c00-2e55-11ea-95c3-4cf51de7382c.png)
- ### 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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.