Page tree

Movie Analysis Folder Setup

If you use the EPU software for data acquisition the hierarchical folder structure can get quite complex. Therefore we link the movies files to a flat folder for better handling of the movie import.

First we create a project and movie folder, then we link the micrograph movies into this folder, finally we check the amount of linked movies:

cdb
mkdir -p MyProject/Movies
cd MyProject/Movies
find ../../supervisor_12345_67890 -name '*.tiff' -size +100M -exec cp -sv {} . \;
ls -1 *.mrcs | wc -l

Note:

  • Make sure that the folder used for the find command contains only movies with the given extension!!! If you merge the EPU metadata with the movie folder it can happen that the folder contains also single-frame MRC files.  Currently files larger than 100MB are movies (-size +100M).

  • The file suffix can change according to your settings like mrcs, mrc, tiff, tif, ...
  • Instead of the relative path ../.. you can use the absolute like /beegfs/cssb/user/username/foldername. You can change this later with the Unix symlinks program.
  • If you move the original movies to a different location, the movie links get broken and you must delete the broken links and recall the find statement above with the new location.

Note: This information below is outdated and is now only valid for Krios1 with the K2 camera!

If you have never worked  in the CSSB environment you can start with the steps as described below.

Create a project directory

mkdir -p /beegfs/cssb/user/${LOGNAME}/MyProject
cd /beegfs/cssb/user/${LOGNAME}/MyProject

The environment variable $LOGNAME contains your login name so a copy&paste from above should work.

Select good micrographs for analysis

Copy all  JPG files from the EPU metadata directory tree to a local directory for easier selection:

epu_prepare_jpg_selection.sh -h
epu_prepare_jpg_selection.sh /beegfs/cssb/group/groupname/microscope_data/krios1_k2/MyProject/Meta

Note:

  • EPU is the technical term for the FEI software.

  • The tool will create a local PreviewSelection folder containing a copy of all EPU metadata JPG files found in the subfolders of the given directory.

  • Now use your favorite JPG viewer software and delete all bad images (Remember you only delete a local COPY of the original files!).

  • Working only with good micrographs saves processing time and you get sooner results.

Link the good micrographs from the EPU micrograph data tree to your local folder for data processing:

epu_prepare_selected_movies.sh -h
epu_prepare_selected_movies.sh /beegfs/cssb/group/groupname/microscope_data/krios1_k2/MyProject/Data

Note:

  • The tool uses the actual file list from the PreviewSelection folder to link the corresponding micrograph movie files into the local Movies folder.
  • The links are Unix symbolic links to the original file location (not a copy)!

    • Deleting the link will not delete the original file! If you move the original files to a new location the link will be broken and must be fixed by hand!
  • Linking the good micrographs works currently only for K2 micrograph names.

  • The tools create also a local Info folder with a list of filenames and patterns.

    • For example the Info/selected_bad_jpg_files.txt file contains a list of deleted JPEG files. It will be used for deleting bad micrograph movies not used in processing to save storage space (not implemented yet!).

Import the selected micrographs into your favorite analysis software:

In your project directory start e.g. relion and import the micrograph movies as described in the Relion tutorial with the pattern Movies/*.mrc.





  • No labels