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/release/3.2.0/html/TOPP_ImageCreator.html
Version: 3.2.0 Sep 18 2024, 16:00:56, Revision: e231942
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 (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

+ImageCreatorTransforms an LC-MS map into an image.

version3.2.0 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 Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false