0 | Number of timeframes (0=all) | default.timeFramesNr
1| Alignment method (1 - nralign) | default.alignMethod
0| Filter the barcodes | default.filterSettingsFilter
0|Add consensus| default.genConsensus
0|Non-default bitmask settings| default.bitmaskSettings
0|Non-default edge detection settings| default.edgeSettings
0|Skip edge detection| default.skipEdgeDetection
0|Generate random fragment cut-outs| default.randomGenerate
0|Generate independent subfragments | default.subfragmentGenerate
1| Global alignment| default.comparisonMethod
150| Minimum length| default.minLen
0.23 | nm/bp extension | default.nmbp
10   | stretch factor max  %    | default.sF
2.5   | stretchfactor step      | default.sFstep
0   | Identify Disc  | default.identifyDisc
1 | Show all output in workspace | default.saveOutput
0 | Save  best-match figures |           default.plotallmatches
0 | Save only discriminative barcode figures |           default.plotalldiscrim
0 | Save infoscores |           default.saveinfoscores
*.tif         |   file extension                                                      | fileext
[3:10 15:19]  | Checklist items | clIdx 
1   | showtheoryimport | showtheoryimport