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BFConvert

Wrapper for the Bioformats command line tool for converting exotic image formats.

Note, that bfconvert has issues with extracting separate channels. It may be a better approach to extract everything and filter later:

        val extr=BFConvert(dir=images, name="%o_C%c_")
        val extr1=Array2Folder(Folder2Array(extr, filePattern=".*_C0_.*"), fileMode="@file@")
        val extr2=Array2Folder(Folder2Array(extr, filePattern=".*_C1_.*"), fileMode="@file@")
    

See command line options, http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/conversion.html, of type "bfconvert" in the command line.

Version 1.0
Bundle anima
Categories Image Processing
Authors Ville Rantanen (ville.rantanen@helsinki.fi)
Issue tracker View/Report issues
Requires bash ; Bioformats bftools ; bc (DEB) ; installer (bash)
Source files component.xml bfconv.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
in BinaryFolder Mandatory Input folder of images, any format recognized by Bioformats library.

Outputs

Name Type Description
out ImageList Output folder of converted TIF images.

Parameters

Name Type Default Description
filter string ".*" Case insensitive filtering of input files with GNU grep (ex. "tif")
gray boolean false Force output images gray scale - sums RGB channels.
multiplier float 1 Multiply output signal. e.g. 12bit camera images need to be multiplied with 4 to use the 16bit image intensity range.
name string "%o_S%s_Z%z_T%t_C%c" Output file name, %o: original input file name, %s: series index, %z: Z section index, %c: channel index, %t: timepoint index, %n series name, %w channel name
png boolean false Convert output to PNG with imagemagick
switches string "" Command line switches to bfconvert.

Test cases

Test case Parameters IN
in
OUT
out
case1 properties in out

switches=-separate -compression LZW,
name=%n_%c

case2_png properties in out

switches=-separate,
png=true,
name=%n_%c


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