OpenMS
Loading...
Searching...
No Matches
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/doxygen/nightly/html/TOPP_ImageCreator.html
Version: 3.6.0-pre-nightly-2026-03-12 Mar 13 2026, 01:45:58, Revision: 88f2819
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

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 [s] (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 TOPP 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

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

  • Name The identifier used in configuration files and on the command line.
  • Default value The value used if the parameter is not explicitly specified.
  • Description A short explanation describing the purpose and behavior of the parameter.
  • Tags Additional metadata associated with the parameter.
  • Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+ImageCreatorTransforms an LC-MS map into an image.
version3.6.0-pre-nightly-2026-03-12 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 [s]
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 Overrides tool-specific checkstrue, false
testfalse Enables the test mode (needed for internal use only)true, false