ilorevilo / lif_summary

easy extraction of microscope images/ videos from a .lif-file

lif_summary

automated extraction of microscope images/ videos from a .lif-file

Since manually exporting acquired entries of Leica .lif-files is quite tedious (especially exporting videos with a defined codec and the correct framerate used for acquisition), this packages provides a simple solution to automatically export all included entries. lif_summary will create a new folder for each .lif-file and extract all images and videos. Exported videos are (at least for my purpose) a useful compromise between compression and quality (e.g. subsequent analysis of beating kinetics of cardiac tissues are feasible in OpenHeartWare. Thanks to readlif, lif-files can be directly accessed in Python. Following exports are currently supported:

• images (xy): export of raw image as .tif, export of image with burned in scalebar + title as .jpg
• multichannel-images (xyc): export of raw multichannel-image as single .tif
• zstacks (xyz): export of raw images as series of .tifs
• videos (xyt): export of video in full resolution and low compression (h.264, crf=17), export of video in max. 1024 px length and higher compression (h.264, crf = 23)

Installation

required packages:

• Python 3
• numpy
• readlif for extracting data from .lif-file
• imageio-ffmpeg providing a pip-installable version of ffmpeg
• PIL and skimage for image operations
• tifffile for writing .tifs
• cv2 for image rescaling operations
• tqdm for progress bars during export

install required packages in your Python environment and run lif_summary.py for any exports

Usage

• Calling python lif_summary.py will export all supported entries from all .lif-files in the current folder
• for more precise export options following syntax can be used:

from lif_summary import lif_summary

inputfile = "path/to/liffile.lif"
summary = lif_summary.lif_summary(inputfile)

summary.export_xy()     # exports all xy-entries
summary.export_xyc()    # exports all xyc-entries
summary.export_xyz()    # exports all xyz-entries
summary.export_xyt()    # exports all xyt-entries
summary.export_all()    # convenience function calling all of the export options above

Changelog

2.0

• switching reader to readlif for a python-only based lif-interface, no need to call bioformats via javabridge anymore
• video exports are now handled by directly piping frames to ffmpeg yielding more precise control of the output video codec and compression
• videos are now exported in full res and low compression as well as in max. 1024 px sidelength and higher compression
• introduce export of extractionlog + raw metadata (xml)
• popwerpoint-creation not supported yet

1.0

• first stable release allowing the export of simple images, videos, zstacks and multichannel-images
• lif-files are accessed by bioformats via javabridge, videos exported by OpenCV (cv2)
• creation of a .ppt-summary of exported images