Up: Component summary Component

ConvertImage

Reads various image formats with LOCI Bioformats library (http://www.loci.wisc.edu/software/bio-formats). Saves each given channel number as a grayscale 16-bit PNG image. .TIF, .PNG, .ZVI, .LSM and .LIF are tested and supported.

SourceOutput

Version 1.2
Bundle anima
Categories Image Transformation
Authors Ville Rantanen (ville.rantanen@helsinki.fi)
Issue tracker View/Report issues
Requires Matlab
Source files component.xml bioformatread.m exoticread.m getexoticimages.m getexoticseries.m execute.m
Usage Example with default values

Inputs

Name Type Mandatory Description
in BinaryFolder Optional A directory with image files.
inArray Array<BinaryFolder> Optional An array of image files.

Outputs

Name Type Description
outArray Array<ImageList> An array of Grayscale PNG images
out ImageList Grayscale PNG images.
list CSV List of images exported.

Parameters

Name Type Default Description
allChannels boolean false Extract all channels and series from all images. Shortcut for defining ch=-1,series=-1
ch float 1 Channel number to read. For RGB images R=1, G=2, B=3. For microscope manufacturer specific formats the number refers to acquisition order. -1 will extract all channels for single series.
depth float 0 Bit depth of the image, if not autodetected (value=0)
group string "" Grouping metadata for the extracted channel.
metadata boolean false Extract all metadata.
nameString string "@ONAME@.@OEXT@_S@S@_C@C@.png" Format of the written file name. Possible keywords: @ONAME@,@OEXT@,@S@,@C@,@GROUP@,@N@ (running index).
series float 1 Image series, if choosing stack levels from multi-page image or animations. -1 for all series from single channel.

Test cases

Test case Parameters IN
in
IN
inArray
OUT
outArray
OUT
out
OUT
list
case1 properties in (missing) (missing) out (missing)

ch=2

case2 properties in (missing) (missing) out list

ch=2,
allChannels=true,
group=test,
nameString=@ONAME@.@OEXT@_S@S@_C@C@_@GROUP@.png

case3_array properties (missing) inArray (missing) out (missing)

ch=2


Generated 2018-12-12 07:42:05 by Anduril 2.0.0