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Make plugins callable from Macro - #3
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@hansenjn hansenjn released this 26 Jul 04:30
· 16 commits to master since this release
v0.3.0
03d3e0b

New features

Fixing request/issue #3, from now on the plugins MotiQ Thresholder, MotiQ 3D Analyzer, MotiQ 2D Analyzer can be launched from a macro to process an active image. Recording the commands with the Macro recorder does not work yet and will be implemented in the future. However, all commands that can be used are included in the example macro calls below. To deselect the boolean commands such as local-threshold or include-date simply remove them from the command string. You can modify the values after the = signs to the settings you wish to use.

run("MotiQ Thresholder (v0.2.0)", "use-alternate automatically-find begin-of-suffix=[_CUT] additional-suffix=[.tif] restrict scale=0.5 convert threshold=MinError stack-handling=[apply threshold determined in a maximum-intensity-projection] threshold-every-time-step threshold-only-distinct-times start-time=1 end-time=10 local-threshold local-threshold-radius=5 fill-holes keep-intensities automatically-save include-date");

run("MotiQ 2D Analyzer (v0.2.0)", "re-calibrate length=0.5 calibration-unit=micron time-interval=0.10 time-unit=min minimum-particle-area=50 remove-all-but-largest time-steps-grouped=12 calculate=[every particle seperately (track particles by overlap)] skeleton=[derive skeleton data from a BINARIZED copy of the input image] gauss=1.0 number-format=[US (0.00...)] include-date");

run("MotiQ 3D Analyzer (v0.3.0)", "re-calibrate length=0.4170 depth=1.0000 calibration-unit=um time-interval=0.50 time-unit=min minimum-particle-volume=50 time-steps-grouped=10 calculate=[all detected particles merged into one object] skeleton=[derive skeleton from a copy of the input image] gauss-xy=1.0 gauss-z=0.0 number-format=[US (0.00...)] include-date");

Bug fixes

In the previous version of MotiQ Thresholder there was a bug in the Fill holes function when processing stacks. The plugin prompted the user when inverting images and asked whether the whole stack should be processed. Also the fill holes function depending on a setting of ImageJ (Process - Binary - Options... -> Black Background) did not work and did rather remove cells than filling holes in cells. These bugs are now fixed.

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