OpenMS
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: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
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-pre-nightly-2024-07-21 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