Executes the top-hat filter to remove the baseline of an MS experiment.

pot. predecessor tools	→ BaselineFilter →	pot. successor tools
NoiseFilterSGolay, NoiseFilterGaussian	→ BaselineFilter →	PeakPickerHiRes (or ID engines on MS/MS data)

This nonlinear filter, known as the top-hat operator in morphological mathematics (see Soille, ''Morphological Image Analysis''), is independent of the underlying baseline shape. It is able to detect an over brightness even if the environment is not uniform. The principle is based on the subtraction of a signal from its opening (erosion followed by a dilation). The size the structuring element (here a flat line) being conditioned by the width of the lineament (in our case the maximum width of a mass spectrometric peak) to be detected.

Note: The top-hat filter works only on roughly uniform data! To generate equally-spaced data you can use the Resampler.; The length (given in Thomson) of the structuring element should be wider than the maximum peak width in the raw data.

The command line parameters of this tool are:

BaselineFilter -- Removes the baseline from profile spectra using a top-hat filter.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_BaselineFilter.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
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:
  BaselineFilter <options>

Options (mandatory options marked with '*'):
  -in <file>*                Input raw data file  (valid formats: 'mzML')
  -out <file>*               Output raw data file  (valid formats: 'mzML')
  -struc_elem_length <size>  Length of the structuring element (should be wider than maximal peak width - 
                             see documentation). (default: '3.0')
  -struc_elem_unit <unit>    Unit of 'struc_elem_length' parameter. (default: 'Thomson') (valid: 'Thomson', 
                             'DataPoints')
  -method <string>           The name of the morphological filter to be applied. If you are unsure, use the 
                             default. (default: 'tophat') (valid: 'identity', 'erosion', 'dilation', 'opening
                             ', 'closing', 'gradient', 'tophat', 'bothat', 'erosion_simple', 'dilation_simple
                             ')
                             
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.

+BaselineFilterRemoves the baseline from profile spectra using a top-hat filter.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'BaselineFilter'

in input raw data file input file*.mzML

out output raw data file output file*.mzML

struc_elem_length3.0 Length of the structuring element (should be wider than maximal peak width - see documentation).

struc_elem_unitThomson Unit of 'struc_elem_length' parameter.Thomson, DataPoints

methodtophat The name of the morphological filter to be applied. If you are unsure, use the default.identity, erosion, dilation, opening, closing, gradient, tophat, bothat, erosion_simple, dilation_simple

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