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README.md

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In a nutshell

Although FEI's EPU can write out whole gain-uncorrected movies now, the compression options are still limited to bit-packed 2 or 4 bit/px MRCs. This tool can be run in the background during acquisition, and will read newly acquired movies, save them as LZW-compressed TIFFs at the specified location or just move them, and (optionally) delete the originals.

You will need

Usage

  • Download everything from the bin directory and put it into a local folder.

  • Run stacker2.exe.

  • Enter the path to the folder containing the individual frames, e. g. Z:\EPU\micrographs.

  • Specify whether the tool should search all sub-folders recursively for new movies.

  • Specify whether the movies should be compressed at all, or just moved to the specified location.

  • In case you just want to move files without compressing them, specify the input file extension (for compression, the input is always *.mrc)

  • Specify the number of frames per movie, e. g. 40. This ensures only files with the correct number of frames are processed.

  • Specify whether the original files should be deleted, or moved to a subfolder named 'original'.

  • Specify whether the gain reference files saved by newer EPU versions for each movie should be deleted automatically.

  • That's it! The tool will now run until you manually close it. While active, it will monitor the folder for new movies, and save them as compressed TIFF files.

  • IMPORTANT #1: If specified, the original files will be deleted once the corresponding output file has been saved successfully.

  • IMPORTANT #2: Compressing data acquired in integrating mode (e. g. Falcon II/III) won't provide significant gains and most likely isn't worth the overhead.

  • IMPORTANT #3: Reading bit-packed MRCs (i. e. 2 or 4 bit/px) isn't supported!

Authorship

Stacker2 is being developed by Dimitry Tegunov (tegunov@gmail.com), currently in Patrick Cramer's lab at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany.