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aim_import takes the following commandline arguments:
Read the slides (id, green tiff, red tiff,[ more tiffs]) from file input-table. Reads from stdin if input-table is -. If the tiff file names contain the configured/supplied tiff directory prefix, the prefix is removed.
list of column separator chars for input table. Defaults to ASCII space and tabulator
Project identifier for the imported data
Add to existing project rather than replace it [Unimplemented]
Specifiy the numbers of columns and rows per grid.
Specifiy the numbers of columns and rows of grids in the layout, i.e. tips in the print head.
Specifies the scanning resolution of the TIFF images in mu-meters per pixel.
AIMProjectsXML file for output. If this file exists already and containts other projects, aim_import adds the new project to the existing entries. An entry which has the same name as given with -p will be replaced, unless -a is given
microarray [ -x projectsxml ] [ -p projectid [ -s slideid ] ] [ -S ] [ --min-nnd lessthanspotdistance ] [ --mrf-local-hcf ] [ --regularity-shortrange ] takes the following commandline arguments:
Select project for gridding
Select slide for gridding
AIMProjectsXML file containing project and slide information
Use active contour method for spot detection in MRF gridding. Slow, but usually improves results.
Use local HCF algorithm variant instead of standard HCF algorithm for MRF energy minimization. May have substantial influence on results.
Calculate regularity score using only directly adjacent grids instead of complete rows and columns of grid blocks.
Tweak grid constant estimation to discard small values. This may be necessary for noisy images with few bright spots and spot distances of more than about 25 pixels. Set the parameter to a value slightly smaller than the true spot distance.
Specify scanned quantile levels in peak histograms for initial region segmentation.
Depending on whether -p or additional -s options are given, microarray traverses the AIMProjects tree of projects, only one project in the tree or just picks one slide (leaf in the tree) for gridding.
aim_quant -p projectid -s slideid [ -S (S|M|C) ] takes the following commandline arguments:
File name for output data, formatted as AIMGriddingXML.
Choose signal segmentation method:
S: Use active contour segmentation.
M: Use Mann-Whitney segmentation. Mann-Whitney test confidence level can be set using the -c option.
C: Use circle segmentation. Circle radius is set do median region radius for all spots
Project identifier of the slide to be analyzed
Slide identifier of the slide to be analyzed
Make a pnm image with all signal pixels set to 1, background pixels 0.
xml2gpr ( -p [ -s slideid ] [ -W input-workdir ] [ -w output-workdir ] | -g in-xml -o out-gpr )
takes the following commandline arguments: (Either -g/-o or -p/-s/-W/-w may be used)
File name for input data, formatted as AIMGriddingXML.
File name for output data, formatted as AIMGriddingXML.
Project identifier of the slide to be analyzed
Slide identifier of the slide to be analyzed
Root of work directory tree from which input files are read
Work directory into which GPR output files are placed (not the root this time).