MicroManager PolScope (plugin) User Manual
Contents
1. ImagejMacro Pre Post Processing Plugin 1 Page ImagejMacro Pre Post Processing Plugin for OpenPolScope software ImagejMacro processing with Pol Acquisition and Pol Analyzer plugin v 2 0 Last Modified April 16 2013 Revision 1 00 Copyright license and warranty disclaimer statements at end of document Table of Contents BEA A TE oat seu pies E E gutesaic esta A E E E E 2 Selecting Processing IMAGEJMACKO csccccsssecccssecccessceccesccecesececeuececeeseesseseceeeeecessueeeeeeeseeeeees 2 OVERVIEW OF OD UONS oistevscaraceeassveviseacesusscusaseiesvaradedadeessinancesuessesarutvsidiadedsuacaitnessiaacasanedpianteatsenieeas 3 Copyright license warranty GisclaiMels cccccccccccsssesceeccsssceeeeeeececeessseeeeeeeeeecessseuuuueeeeeeseuenes 3 ImagejMacro Pre Post Processing Plugin 2 Page Overview A macro is a simple program that automates a series of ImageJ commands More information can be found here http rsbweb nih gov ij developer macro macros html Eg 1 PreProcessor Macro for Pol Acquistion Pol Analyzer setFont SansSerif 50 antialiased setColor black drawString Pre Processed 100 100 r ri Gaussian Blur Ssigma 2 slice Eg 2 PostProcessor Macro for Pol Acquistion Pol Analyzer setFont SansSerit 50 antialiased gt setColor white drawString Post Processed 100 200 The above two codes are examples of ImageJ macro files Eg 1 first wri2. t Macro PreProchiacro ijm Edit Apply to Sample Applies the selected macro to the Sample dataset when running Process or Acquisition Apply to Background Applies the selected macro to the Background dataset when running Process or Acquisition All Channels Applies the selected Macro to all channels in the dataset If a channel specific macro is selected this selection should be disabled Edit The selected macro will open in an editable text window PreProcMacro yjm WELES ee ee eee i PreProcessor Macro for Pol Acquistion PolAnalyzer setFont SansSerif 50 antialiased setColor black drawstring Pre Processed 100 100 ImagejMacro Pre Post Processing Plugin 4 Page Copyright license warranty disclaimer Copyright 2009 2013 Marine Biological Laboratory NOTICE Some of the algorithms herein are protected by US patent 5521705 7202950 and other patents applied for or pending LICENSE Berkeley Software Distribution License Redistribution and use in source and binary forms with or without modification are permitted provided that the following conditions are met 1 Redistributions of source code must retain the above copyright notice this list of conditions and the following disclaimer 2 Redistributions in binary form must reproduce the above copyright notice this list of conditions and the following disclaimer in the documentation and or other materials provided with the distribu
3. tes the text Pre Processed on the raw image and then performs a Gaussian Blur on the raw image Eg 2 first writes the text Post Processed in white on the computed image Note The distinction between Pre amp Post in context to Pol Acquisition amp Pol Analyzer is that a Pre macro affects the Raw images and the Post macro affects the Computed images There are a number of built in functions available in imageJ that can be utilized http rsobweb nih gov ij developer macro functions html On top of that any third party plugin installed in imageJ that supports macro commands can also be utilized http rsb info nih gov ij plugins index html Additional examples of imageJ macro s can be found here http rsb info nih gov ij macros Once the sample is acquired or re processed the ImagejMacro filename is inserted in the image metadata Od m p ELT E T LO T E T A i O l e L T iie m T I G El A e summary es 1 BlackLevel 0 Interval _ms 0 UL Summary OOOO oO deve O terval sO UL os PreProcMacro ijm ImagejMacro Pre Post Processing Plugin 3 Page Selecting Processing ImagejMacro On the Pol Acquisition or Pol Analyzer interface select the checkbox corresponding to the ImagejMacro Pre Post Processing plugin If ImagejMacro is not listed as available then you may need to install it via the OpenPolScope Setup Pre Processing Enabled Description Options a E imagejMacro Pre CAMICRO 1 _4 macros Selec
4. tion 3 Neither the name of the Marine Biological Laboratory nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT INDIRECT INCIDENTAL SPECIAL EXEMPLARY OR CONSEQUENTIAL DAMAGES INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES LOSS OF USE DATA OR PROFITS OR BUSINESS INTERRUPTION HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY WHETHER IN CONTRACT STRICT LIABILITY OR TORT INCLUDING NEGLIGENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies either expressed or implied of any organization From the Laboratory of Rudolf Oldenbourg rudolfo mbl edu Cellular Dynamics Program Marine Biological Lab Woods Hole MA USA 2013 Lab Webpage
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