diff --git a/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm b/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm index 797a6ec4f7d7860f0d87db70366fe48134e5d30c..3596021f81b6cd38dbea1d07e52afa39c3b996fd 100644 --- a/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm +++ b/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm @@ -1,16 +1,3 @@ -// #@ String (visibility=MESSAGE, label="NoiSee -", value="Beads SNR analysis", persist=false) msg_title -// @File(label="Beads time-series image",description="2D time-lapse acquisition of fluorescent beads") beadsimage -// @Integer(label="Beads diameter (in pixels)",description="approximate bead diameter (in pixels)",value=15) beads_diameter -// @Integer(label="Find Maxima noise tolerance",description="typical values: [PMT=50] [HyD (photon counting)=10] [Camera=500]",value=50) beads_noisetolerance -// @Boolean(label="Create Kymographs",description="visual indicator for drift and bleaching",value="true") make_kymographs -// @Boolean(label="Save additional measurements",description="store 'StdDev', 'SNR', 'Mean' and 'bleaching' measurements",value="false") save_measurements -// @Boolean(label="Save results as PDF",description="generate a PDF with images and plots",value="true") save_pdf -// @Boolean(label="Keep ROI images open",description="if disabled ROI visualizations will only be added to PDF",value="false") keep_roiimages -// @Integer(label="Log level",description="higher number means more messages",min=0,max=2,style="scroll bar") LOGLEVEL -// @Boolean(label="Save log messages",description="save contents of the 'Log' window in a text file",value="false") save_log -// #@ String (visibility=MESSAGE, label="Note:", value="all currently open images will be closed", persist=false) msg_note_close - - //////////// NoiSee Beads Analysis /////////////////////////////////////////////////////// // SNR evaluation macro, written by Kai Schleicher, Niko Ehrenfeuchter, IMCF Basel // licence: GPLv3 @@ -27,6 +14,25 @@ // - "roi_" - index number of a ROI manager entry +//////// Script Parameters, see https://imagej.net/Script_Parameters for details +#@ String (visibility=MESSAGE, label="NoiSee -", value="Beads SNR analysis", persist=false) msg_title +#@ File(label="Beads time-series image",description="2D time-lapse acquisition of fluorescent beads") beadsimage +#@ Integer(label="Beads diameter (in pixels)",description="approximate bead diameter (in pixels)",value=15) beads_diameter +#@ Integer(label="Find Maxima noise tolerance",description="typical values: [PMT=50] [HyD (photon counting)=10] [Camera=500]",value=50) beads_noisetolerance +#@ Boolean(label="Create Kymographs",description="visual indicator for drift and bleaching",value="true") make_kymographs +#@ Boolean(label="Save additional measurements",description="store 'StdDev', 'SNR', 'Mean' and 'bleaching' measurements",value="false") save_measurements +#@ Boolean(label="Save results as PDF",description="generate a PDF with images and plots",value="true") save_pdf +#@ Boolean(label="Keep ROI images open",description="if disabled ROI visualizations will only be added to PDF",value="false") keep_roiimages +#@ String (visibility=MESSAGE, label="Note:", value="all currently open images will be closed", persist=false) msg_note_close + + +// valid log levels: 0 (quiet), 1 (info messages), 2 (debug messages) +LOGLEVEL=0; + +// save contents of the 'Log' window in a text file: +save_log=false; + + ////////////////// function definitions /////////////////////////////// function duplicateImage(id_orig, new_name, single){ diff --git a/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Fluorescein_Analysis.ijm b/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Fluorescein_Analysis.ijm index 79bff0ee36e0114e8d59f9751b31c8f601956510..df3054dab206148a753acd39ad769429d064b95c 100644 --- a/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Fluorescein_Analysis.ijm +++ b/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Fluorescein_Analysis.ijm @@ -1,12 +1,3 @@ -// #@ String (visibility=MESSAGE, label="NoiSee -", value="Fluorescein SNR analysis", persist=false) msg_title -// @File(label="Dark image",description="dark field image (i.e. 'laser off')") darkimage -// @File(label="Fluorescein image",description="image of a homogeneous fluorescent solution") fluoimage -// @Boolean(label="Save results as PDF",description="generate a PDF with images and results",value="true") save_pdf -// @Integer(label="Log level",description="higher number means more messages",min=0,max=2,style="scroll bar") LOGLEVEL -// @Boolean(label="Save log messages",description="save contents of the 'Log' window in a text file",value="false") save_log -// #@ String (visibility=MESSAGE, label="Note:", value="all currently open images will be closed", persist=false) msg_note_close - - //////////// NoiSee Fluorescein Analysis /////////////////////////////////////////////////////// // SNR evaluation macro, written by Kai Schleicher, Niko Ehrenfeuchter, IMCF Basel // licence: GPLv3 @@ -19,6 +10,21 @@ // - "rgb_" - image IDs of 2D RGB images +//////// Script Parameters, see https://imagej.net/Script_Parameters for details +#@ String (visibility=MESSAGE, label="NoiSee -", value="Fluorescein SNR analysis", persist=false) msg_title +#@ File(label="Dark image",description="dark field image (i.e. 'laser off')") darkimage +#@ File(label="Fluorescein image",description="image of a homogeneous fluorescent solution") fluoimage +#@ Boolean(label="Save results as PDF",description="generate a PDF with images and results",value="true") save_pdf +#@ String (visibility=MESSAGE, label="Note:", value="all currently open images will be closed", persist=false) msg_note_close + + +// valid log levels: 0 (quiet), 1 (info messages), 2 (debug messages) +LOGLEVEL=0; + +// save contents of the 'Log' window in a text file: +save_log=false; + + ////////////////// function definitions /////////////////////////////// function duplicateImage(id_orig, new_name, single){