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5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Cambria","serif"; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin;} </style> <![endif]--><!--[if gte mso 9]><xml> <o:shapedefaults v:ext="edit" spidmax="1026"/> </xml><![endif]--><!--[if gte mso 9]><xml> <o:shapelayout v:ext="edit"> <o:idmap v:ext="edit" data="1"/> </o:shapelayout></xml><![endif]--> </head> <body lang=EN-US link=blue vlink=purple style='tab-interval:36.0pt'> <div class=WordSection1> <p class=MsoPlainText style='margin-left:13.5pt;mso-outline-level:1'><span style='font-size:9.0pt;font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'>Go back to </span><a href="http://simon.bio.uva.nl/objectj/7a-Examples.html"><span style='font-size:9.0pt;font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'>ObjectJ Examples</span></a><span style='font-size:9.0pt;mso-bidi-font-size:10.5pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:14.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;mso-outline-level:1'><span style='font-size:14.0pt;font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'>Marking and categorizing oocytes</span><span style='font-size:14.0pt;mso-bidi-font-size: 12.0pt;font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'>&nbsp;</span><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>Version 27<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>01-apr-2010<span style="mso-spacerun:yes">    </span>vischer at science.uva.nl<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>This project allows automatic and manual measurements of oocyte cells.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>Resulting parameters are cell size and elliptical aspect ratio. Size<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>is visualized by a red line indicating the diameter of equivalent circle with same area.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>A category (1..9) can be added manually, and is visualized by the &quot;hand of a clock&quot;.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>You can get statistics of any subset of objects that meets a combination of properties<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoPlainText style='margin-top:0cm;margin-right:124.75pt;margin-bottom: 0cm;margin-left:13.5pt;margin-bottom:.0001pt;tab-stops:609.55pt'><span style='font-size:9.0pt;font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoPlainText style='margin-top:0cm;margin-right:124.75pt;margin-bottom: 0cm;margin-left:13.5pt;margin-bottom:.0001pt;mso-outline-level:1;tab-stops: 609.55pt'><a href="http://simon.bio.uva.nl/objectj/examples/oocytes/oocytes-project/"><span style='font-size:9.0pt;font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'>Download oocytes project</span></a><span style='font-size:9.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'> <span style="mso-spacerun:yes"> </span><o:p></o:p></span></p> <p class=MsoPlainText style='margin-top:0cm;margin-right:124.75pt;margin-bottom: 0cm;margin-left:13.5pt;margin-bottom:.0001pt;mso-outline-level:1;tab-stops: 609.55pt'><span style='font-size:9.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoPlainText style='margin-top:0cm;margin-right:124.75pt;margin-bottom: 0cm;margin-left:13.5pt;margin-bottom:.0001pt;mso-outline-level:1;tab-stops: 609.55pt'><span style='font-size:9.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>Watch the </span><a href="http://simon.bio.uva.nl/objectj/examples/oocytes/oocytes-a.mov"><span style='font-size:9.0pt;font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'>movie</span></a><span style='font-size:9.0pt;mso-bidi-font-size:10.5pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'>&nbsp;</span><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f"> <v:stroke joinstyle="miter"/> <v:formulas> <v:f eqn="if lineDrawn pixelLineWidth 0"/> <v:f eqn="sum @0 1 0"/> <v:f eqn="sum 0 0 @1"/> <v:f eqn="prod @2 1 2"/> <v:f eqn="prod @3 21600 pixelWidth"/> <v:f eqn="prod @3 21600 pixelHeight"/> <v:f eqn="sum @0 0 1"/> <v:f eqn="prod @6 1 2"/> <v:f eqn="prod @7 21600 pixelWidth"/> <v:f eqn="sum @8 21600 0"/> <v:f eqn="prod @7 21600 pixelHeight"/> <v:f eqn="sum @10 21600 0"/> </v:formulas> <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/> <o:lock v:ext="edit" aspectratio="t"/> </v:shapetype><v:shape id="_x0000_i1026" type="#_x0000_t75" style='width:321pt; height:235pt;visibility:visible;mso-wrap-style:square'> <v:imagedata src="Oocytes_files/image001.png" o:title=""/> </v:shape><![endif]--><![if !vml]><img border=0 width=323 height=237 src="Oocytes_files/image002.png" v:shapes="_x0000_i1026"><![endif]></span><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'>&nbsp;</span><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;mso-outline-level:1'><b style='mso-bidi-font-weight:normal'><i style='mso-bidi-font-style:normal'><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>A - Install ObjectJ<o:p></o:p></span></i></b></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>1.<span style='mso-tab-count:1'>    </span>Download ObjectJ from http://simon.bio.uva.nl/objectj/<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>go to &quot;download&quot; and choose the version with the<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style="mso-spacerun:yes"> </span>highest number, currently ObjectJ 1.01n)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>2.<span style='mso-tab-count:1'>    </span>put objectj_.jar into the plugins folder of the ImageJ folder<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>3.<span style='mso-tab-count:1'>    </span>Restart ImageJ<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>4.<span style='mso-tab-count:1'>    </span>choose menu Plugins&gt;ObjectJ<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>5.<span style='mso-tab-count:1'>    </span>Now the menu bar should show &quot;ObjectJ&quot; (between &quot;Analyze&quot; and &quot;Plugins&quot;)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>6.<span style='mso-tab-count:1'>    </span>(Next time, ObjectJ can be upgraded simultaneously with ImageJ<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>via: menu Help&gt;Update ImageJ)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;mso-outline-level:1'><b style='mso-bidi-font-weight:normal'><i style='mso-bidi-font-style:normal'><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>B - Download Sample Project<o:p></o:p></span></i></b></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>1.<span style='mso-tab-count:1'>    </span>Download oocytes-27<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>(version number may be higher)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><span style="mso-spacerun:yes"> </span><span style='mso-tab-count:1'>      </span>Folder contains:<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>project file= oocytes-27.ojj<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>Anchovy_oocytes.jpg<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><span style="mso-spacerun:yes">        </span>Fec 5.jpg<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>2.<span style='mso-tab-count:1'>    </span>Make sure these files are in the same folder<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>after unpacking, we call it the &quot;project folder&quot;. You can replace<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>the sample image by any number of your own images<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>3.<span style='mso-tab-count:1'>    </span>Drag the .ojj file into the ImageJ main window to<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>open this project, wait until the project window <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:22.5pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>appears showing the names of &quot;Linked Images&quot;<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt;text-indent:14.85pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>(Alternatively, choose menu ObjectJ&gt;Open Project..).<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:13.5pt'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:63.8pt'><b style='mso-bidi-font-weight:normal'><i style='mso-bidi-font-style: normal'><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><span style="mso-spacerun:yes"> </span><o:p></o:p></span></i></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:63.8pt'><b style='mso-bidi-font-weight:normal'><i style='mso-bidi-font-style: normal'><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'>C - Usage<o:p></o:p></span></i></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>1. <span style='mso-tab-count:1'> </span>Automatic marking of diameters<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count: 1'>     </span>-<span style="mso-spacerun:yes">  </span>chose menu ObjectJ&gt;Mark Oocytes...<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count: 1'>     </span>- In the dialog, if threshold is set to zero, you are asked to<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count: 1'>     </span><span style="mso-spacerun:yes">   </span>threshold each image interactively.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_1" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:191pt; height:130pt;visibility:visible;mso-wrap-style:square'> <v:imagedata src="Oocytes_files/image003.png" o:title=""/> </v:shape><![endif]--><![if !vml]><img border=0 width=193 height=132 src="Oocytes_files/image004.png" v:shapes="Picture_x0020_1"><![endif]></span><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 63.8pt'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family: "Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>2.<span style='mso-tab-count:1'>  </span><b style='mso-bidi-font-weight:normal'>Categorize any marked cell</b><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-<span style='mso-tab-count:1'>   </span>With no Roi visible, locate the cursor above a marked cell and press<o:p></o:p></span></p> <p class=MsoNormal style='tab-stops:1.0cm'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><span style='mso-tab-count:1'>         </span>key 1..9 for category. Cell will obtain that category as hand of a clock<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>(e.g. 4 o'clock is category 4), - or cell will <o:p></o:p></span></p> <p class=MsoNormal style='tab-stops:1.0cm'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><span style='mso-tab-count:1'>         </span>be killed if 0 is pressed. (You also could kill a cell<o:p></o:p></span></p> <p class=MsoNormal style='tab-stops:1.0cm'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'><span style='mso-tab-count:1'>         </span>with the pistol tool).<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>3.<span style='mso-tab-count:1'>  </span>Label cell only without measuring it<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>A a line of fixed length (185 um at 45 deg) is used to <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>mark the existence of a cell type.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-<span style='mso-tab-count:2'>      </span>Choose menu ObjectJ&gt;Fixed Diameter [F] (or select<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>the &quot;F&quot; button in the ObjectJ tools window).<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>Then, click on the center of a cell to mark it.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>4. <span style='mso-tab-count:1'> </span>Show/Hide floating circle<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>A floating circle that follows the cursor movement<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>can help to visually estimate cell sizes. It's diameter is 185 um.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:2'>     </span>Choose<span style="mso-spacerun:yes">  </span>ObjectJ&gt;Variable Diameter (toggle circle) [V],<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>or press &quot;V&quot; key.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>This activates the &quot;V&quot; tool in the ObjectJ Tools window;<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>and switches the floating circle on or off. If the mouse rests for<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>10 sec, the floating circle will be switched off.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>You can press V again to switch it on again.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>5. <span style='mso-tab-count:1'> </span>Show/Hide Ellipses<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Shows or hides the ellipse items of marked cells.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>6. <span style='mso-tab-count:1'> </span>Manually marking of ellipses:<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:2'>     </span>make sure the variable ellipse tool (button marked with &quot;V&quot;) in ObjectJ Tools is selected<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:2'>     </span>click and drag along a line A-B to follow the ellipse major axis (or<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>diameter in case of a circle).<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>After releasing the mouse, a circular roi is shown. <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-<span style='mso-tab-count:2'>      </span>if you want to leave this circular roi as such,<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>move the cursor further outside until the roi flashes<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:2'>     </span>otherwise, if you want to change the circle into an ellipse, then move the cursor back <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>inside, which decreases the minor axis. During this phase, you also can<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>fine-adjust the orientation.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>Now you need a second mouse-down click to confirm the current ellipse.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>Before again releasing the mouse button, you can re-adjust the ellipse's position.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-<span style='mso-tab-count:2'>      </span>At any moment during ellipse editing, you can press any category key (1..9)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>to finalize and categorize the ellipse.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>7. <span style='mso-tab-count:1'> </span>Convert ellipse roi into marked and categorized cell<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:2'>     </span>when an elliptical roi is visible, it can be marked and categorized with<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>key 1..9. After that, the &quot;V&quot; tool remains activated.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt; mso-bidi-font-size:12.0pt;font-family:"Lucida Grande";mso-bidi-font-family: "Times New Roman"'>8.<span style='mso-tab-count:1'>  </span>Categorizing marked cells sequentially:<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>This mode is intended to visit marked cells in sequence (1, 2, 3..), <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>in order to categorize them.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-<span style='mso-tab-count:2'>      </span>The sequential modus is active when<span style="mso-spacerun:yes">  </span>a halo visible. The halo is <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>symbolized by two concentric rois.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>The inner roi corresponds to the diameter of the selected cell, the<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span>outer roi is used for &quot;zoom to selection&quot; <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:1'>  </span>You can enter the sequential modus by locating the cursor <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>above a marked cell (e.g. cell 17) and press the &quot;Q&quot; key, that corresponds to<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Toggle Sequential Mode [Q]<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>The halo now highlights cell 17<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>(If the halo was already active, it will disappear)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-<span style='mso-tab-count:1'>   </span>With the halo visible, press any key 1..9 to categorize that <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>cell, or press zero to kill it.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>After 0.25 sec, the halo highlights the next cell (cell 18 in the example).<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-<span style="mso-spacerun:yes">   </span>Use previous [p] or next [n] shortcuts to navigate the halo.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>9.<span style='mso-tab-count:1'>  </span>Applying a default category<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:1'>  </span>You can set a default category to all objects that have no category yet.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>This is done in all linked images.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-<span style='mso-tab-count:1'>   </span>Choose ObjectJ&gt;Categorize all uncategorized cells...<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>and after entering a number, all uncategroized cells will be categorized.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>10.<span style='mso-tab-count:2'>               </span>Results<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:1'>  </span>Choose ObjectJ&gt;Show Project Results<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>to display numeric results. These columns are implemented:<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Dia<span style='mso-tab-count:1'>          </span>equivalent diameter in um<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Cat <span style='mso-tab-count:1'>         </span>category 1..9<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Roundn.<span style='mso-tab-count:1'>  </span>same as Minor/Major (range 0..1)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Ellipt.<span style='mso-tab-count:1'>      </span>ellipticity= ellipse perimeter/actual perimeter <o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:3'>                   </span>(range 0..1, or empty for manual marking)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Minor<span style='mso-tab-count:1'>      </span>minor axis (um)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Major<span style='mso-tab-count:1'>      </span>major axis (um)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>Area3<span style='mso-tab-count:1'>      </span>area (unit is 10^3 um^2 for convenience)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:2'>       </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>11.<span style='mso-tab-count:2'>               </span>Saving<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style='mso-tab-count:1'>  </span>Periodically save the colored markers via menu ObjectJ&gt;Save project.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span>(Note that menu &quot;File&gt;Save&quot; only saves an image, not the markers)<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style='mso-tab-count:1'>     </span><o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>12.<span style='mso-tab-count:2'>               </span>Mark your own images<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-&nbsp; once the described sample project works satisfactory, you can save an empty copy<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><span style="mso-spacerun:yes">    </span>of the project file via ObjectJ&gt;Project File&gt; Save an Empty Copy& <span style="mso-spacerun:yes">  </span>and relaunch ImageJ.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- The empty copy contains all internal structure and macros, but no markers or linked images.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- <span style="mso-spacerun:yes"> </span>Link your images via ObjectJ&gt;Linked Images&gt; Link Image from project Folder<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- Make sure your linked images are scaled correctly (eg pixels per um)<o:p></o:p></span></p> <p class=MsoNormal><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;mso-outline-level: 1;tab-stops:1.0cm'><b style='mso-bidi-font-weight:normal'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>13.<span style='mso-tab-count:2'>               </span>Notes<o:p></o:p></span></b></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>-&nbsp;cells with fixed diameters don't have any quantitative result entries.<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- category 0 cannot be applied, it is rather used to delete an object under the cursor<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- marking a cell with &quot;fixed diameter&quot; does not invite to add a category<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:1.0cm;text-indent:-14.85pt;tab-stops: 1.0cm'><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt;font-family:"Lucida Grande"; mso-bidi-font-family:"Times New Roman"'>- Categorize all unmarked cells also categorizes those with fixed diameter<o:p></o:p></span></p> <p class=MsoNormal><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal><span style='font-size:9.0pt;mso-bidi-font-size:12.0pt; font-family:"Lucida Grande";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal><span style='mso-ascii-font-family:Cambria;mso-ascii-theme-font: minor-latin;mso-fareast-font-family:"-ÿ3ÿ fg";mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Cambria;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: "Times New Roman";mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p> </div> </body> </html>