OpenMS  2.5.0
ImageCreator

Transforms an LC-MS map into a png image.

The input is first resampled into a matrix using bilinear forward resampling. Then the content of the matrix is written to an image file. The output has a uniform spacing in both dimensions regardless of the input.

The command line parameters of this tool are:


ImageCreator -- Transforms an LC-MS map into an image.

Full documentation: http://www.openms.de/documentation/UTILS_ImageCreator.html

Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

To cite OpenMS:

  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.



Usage:

  ImageCreator <options>



Options (mandatory options marked with '*'):

  -in <file>*                Input file  (valid formats: 'mzML')

  -in_featureXML <file>      Input file  (valid formats: 'featureXML')

  -out <file>*               Output file (valid formats: 'png', 'jpg', 'bmp', 'tiff', 'ppm')

  -out_type <file type>      The image format. Set this if you want to force a format not reflected by the 

                             'out' filename. (valid: 'png', 'jpg', 'bmp', 'tiff', 'ppm')

  -rt [min]:[max]            Retention time range to extract (default: ':')

  -mz [min]:[max]            Mass-to-charge range to extract (default: ':')

  -width <number>            Number of pixels in m/z dimension.

                             If 0, one pixel per Th. (default: '1024' min: '0')

  -height <number>           Number of pixels in RT dimension.

                             If 0, one pixel per spectrum. (default: '1024' min: '0')

  -background_color <color>  Background color e.g.: "#FF0000" to choose red as background color (default: 

                             '#FFFFFF')

  -feature_color <color>     Feature color e.g.: "#00FF00" to choose green as feature color (default: '#00000

                             0')

  -gradient <gradient>       Intensity gradient that defines colors for the range between 0 and 100.

                             Example: '0,#FFFFFF;50,#FF0000;100,#000000'

  -max_intensity <int>       Maximum peak intensity used to determine range for colors.

                             If 0, this is determined from the data. (default: '0.0')

  -log_intensity             Apply logarithm to intensity values

  -transpose                 Flag to transpose the resampled matrix (RT vs. m/z).

                             Per default, dimensions run bottom-up in RT and left-right in m/z.

  -precursors                Mark locations of MS2 precursors.

                             

  -precursor_color <color>   Color for precursor marks (color code or word, e.g. 'black') (requires 'precurso

                             rs' flag to be active) (default: '#000000')

  -precursor_size <number>   Size of the precursor marks (requires 'precursors' flag to be active) (default: 

                             '2' min: '1' max: '3')

                             

Common UTIL options:

  -ini <file>                Use the given TOPP INI file

  -threads <n>               Sets the number of threads allowed to be used by the TOPP tool (default: '1')

  -write_ini <file>          Writes the default configuration file

  --help                     Shows options

  --helphelp                 Shows all options (including advanced)



INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+ImageCreatorTransforms an LC-MS map into an image.
version2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1Instance '1' section for 'ImageCreator'
in input file input file*.mzML
in_featureXML input file input file*.featureXML
out output fileoutput file*.png,*.jpg,*.bmp,*.tiff,*.ppm
out_type The image format. Set this if you want to force a format not reflected by the 'out' filename.png,jpg,bmp,tiff,ppm
rt: Retention time range to extract
mz: Mass-to-charge range to extract
width1024 Number of pixels in m/z dimension.
If 0, one pixel per Th.
0:∞
height1024 Number of pixels in RT dimension.
If 0, one pixel per spectrum.
0:∞
background_color#FFFFFF Background color e.g.: "#FF0000" to choose red as background color
feature_color#000000 Feature color e.g.: "#00FF00" to choose green as feature color
gradient Intensity gradient that defines colors for the range between 0 and 100.
Example: '0,#FFFFFF;50,#FF0000;100,#000000'
max_intensity0.0 Maximum peak intensity used to determine range for colors.
If 0, this is determined from the data.
log_intensityfalse Apply logarithm to intensity valuestrue,false
transposefalse flag to transpose the resampled matrix (RT vs. m/z).
Per default, dimensions run bottom-up in RT and left-right in m/z.
true,false
precursorsfalse Mark locations of MS2 precursors.
true,false
precursor_color#000000 Color for precursor marks (color code or word, e.g. 'black') (requires 'precursors' flag to be active)
precursor_size2 Size of the precursor marks (requires 'precursors' flag to be active)1:3
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false