OpenMS
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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/3.3.0/html/TOPP_ImageCreator.html Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65 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: