LEICA2TIF convert .lif files to TIFF

Installation

This package is pip installable, but can most easily be installed using Anaconda, e.g.:

wget https://raw.githubusercontent.com/chunglabmit/leica2tif/master/environment.yaml
conda env create -f environment.yaml

Usage

leica2tif \
  --input <lif-file> \
  --output-pattern <output-pattern> \
  [--series <series>] \
  [--z-min <z-min>] \
  [--z-max <z-max>] \
  [--c <channel>] \
  [--t-min <t-min>] \
  [--t-max <t-max>] \
  [--compression <compression>] \
  [--dtype <dtype>]

where

• lif-file is the path to the Leica file.
• output-pattern is a format style file naming pattern, e.g. /path-to/img_{z:04d}-{c:04d}-{t:04d}.tiff. Substitutions are made for z, c (the channel #) and t (the time as an index).
• series the zero-based series # to be read out of the .lif file. A quick trick here is to open the .lif in Fiji and subtract 1 from the series you want.
• z-min read z frames starting at this z (default 0).
• z-max read z frames up until this z (default all z).
• c read this channel index (starting at zero). This may be specified multiple times. Default is to read all channels.
• t-min read time frames starting at this t (default 0).
• t-max read time frames up until this t.
• compression compression level (0-9) for tiffs, defaults to 3.
• dtype is the pixel data type for the output. To convert a floating- point .lif file to 16 bit TIFF, use "--dtype uint16". The data will be scaled from floating point 0-1 to the integer data type.