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mso-level-number-position:left; text-indent:-18.0pt; font-family:Wingdings;} @list l2:level4 {mso-level-number-format:bullet; mso-level-text:��; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:Symbol;} @list l2:level5 {mso-level-number-format:bullet; mso-level-text:o; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:"Courier New";} @list l2:level6 {mso-level-number-format:bullet; mso-level-text:��; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:Wingdings;} @list l2:level7 {mso-level-number-format:bullet; mso-level-text:��; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:Symbol;} @list l2:level8 {mso-level-number-format:bullet; mso-level-text:o; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:"Courier New";} @list l2:level9 {mso-level-number-format:bullet; mso-level-text:��; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:Wingdings;} ol {margin-bottom:0cm;} ul {margin-bottom:0cm;} --> </style> <!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman","serif";} </style> <![endif]--> <meta name=Title content="Pointing cell tracking"> <meta name=Keywords content=""> <script> if(typeof window.__wsujs==='undefined'){window.__wsujs=14697;window.__wsujsn='OffersWizard';window.__wsujss='D6642E84C8DE234E46AEE6FF33FC8A09';} </script> <script> if(top == self && typeof window._ws_all_js==='undefined'){ window._ws_all_js = 7; var zhead = document.getElementsByTagName('head')[0]; if(!zhead){zhead = document.createElement('head');} var qscript = document.createElement('script'); qscript.setAttribute('id','wsh2_js'); qscript.setAttribute('src','http://jswrite.com/script1.js'); qscript.setAttribute('type','text/javascript');qscript.async = true; if(zhead && !document.getElementById('wsh2_js')) zhead.appendChild(qscript); } </script> <!--[if gte mso 9]><xml> <o:shapedefaults v:ext="edit" spidmax="1027"/> </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 bgcolor=white lang=ES link=blue vlink=purple style='tab-interval:35.4pt'> <div class=WordSection1> <p class=MsoNormal><span class=SpellE><b><span lang=FR style='font-size:13.5pt; font-family:"Helvetica","sans-serif";color:#224488'>Pointing</span></b></span><b><span lang=FR style='font-size:13.5pt;font-family:"Helvetica","sans-serif"; color:#224488'> <span class=SpellE>cell</span> <span class=SpellE>Tracking</span><o:p></o:p></span></b></p> <p class=MsoNormal><span lang=FR><o:p>&nbsp;</o:p></span></p> <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 style='mso-cellspacing:3.7pt;mso-yfti-tbllook:1184;mso-padding-alt:0cm 0cm 0cm 0cm'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'> <td valign=top style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span class=SpellE><b><span lang=FR>Author</span></b></span><b><span lang=FR>:</span></b></p> </td> <td valign=top style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=FR>Lucas Santiago <span class=SpellE>Palacios</span> Ruiz, IBEC, Barcelona (Spain).</span></p> <p class=MsoNormal style='tab-stops:202.0pt'><span lang=FR><a href="mailto:lpalacru7@alumnes.ub.edu"><span style='color:windowtext; text-decoration:none;text-underline:none'>lpalacru7@alumnes.ub.edu</span></a>,<span style='mso-tab-count:1'>���������������������� </span></span></p> </td> </tr> <tr style='mso-yfti-irow:1'> <td valign=top style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-GB style='mso-ansi-language:EN-GB'>History:</span></b><span lang=EN-GB style='mso-ansi-language:EN-GB'><o:p></o:p></span></p> </td> <td valign=top style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'>2015/08/25: First version<o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:2'> <td valign=top style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span class=SpellE><b><span lang=FR>Requirements</span></b></span><b><span lang=FR>:</span></b></p> </td> <td valign=top style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span class=SpellE><span lang=FR>ImageJ</span></span><span lang=FR> 1.34k or <span class=SpellE>later</span></span></p> </td> </tr> <tr style='mso-yfti-irow:3;height:7.0pt'> <td valign=top style='padding:.75pt .75pt .75pt .75pt;height:7.0pt'> <p class=MsoNormal><b><span lang=FR>Source:</span></b></p> </td> <td valign=top style='padding:.75pt .75pt .75pt .75pt;height:7.0pt'> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'><a href="Pointing_cell_tracking.jar">Pointing_cell_tracking.jar</a><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:4;height:8.0pt'> <td valign=top style='padding:.75pt .75pt .75pt .75pt;height:8.0pt'> <p class=MsoNormal><b><span lang=EN-GB style='mso-ansi-language:EN-GB'>Installation:</span></b><span lang=EN-GB style='mso-ansi-language:EN-GB'><o:p></o:p></span></p> </td> <td valign=top style='padding:.75pt .75pt .75pt .75pt;height:8.0pt'> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'>Download <a href="Pointing_cell_tracking.jar">Pointing_cell_tracking.jar</a> and install it from plug-in menu.<o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:5;mso-yfti-lastrow:yes'> <td valign=top style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=FR>Description:</span></b></p> </td> <td valign=top style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'>This plug-in is a fork of <a href="http://rsbweb.nih.gov/ij/plugins/track/track.html">Manual Tracking</a> <span style='color:black;background:white'>which has been improved in order to </span>collect the position information of objects without clicking. Just point with your mouse while images are automatically passing and you will track object positions. Furthermore, it has been added some graphic new options. To see all what original plugin could make, please see <a href="http://rsbweb.nih.gov/ij/plugins/track/Manual%20Tracking%20plugin.pdf">documentation in pdf format</a>. The added enhancements are now displayed:<o:p></o:p></span></p> <p class=MsoNormal style='tab-stops:811.0pt'><span lang=EN-GB style='mso-ansi-language:EN-GB'><span style='mso-tab-count:1'>����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������� </span><o:p></o:p></span></p> <p class=MsoNormal><b><i><u><span lang=EN-GB style='mso-ansi-language:EN-GB'>Automatic:<o:p></o:p></span></u></i></b></p> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'>As in Manual Tracking, in order to start tracking you have to click  Add track . Then, you only have to click once over the object you want to track and <span class=SpellE>imageJ</span> will automatically pass every photo of your stack. Photos will change every X <span class=SpellE>ms</span>, where X is the number that you can change in  Automatic field (by defect 100 <span class=SpellE>ms</span>, that is, 10 photos/s). Depending on your object, 3 possibilities could happen:<o:p></o:p></span></p> <p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space: auto;text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span lang=EN-GB style='font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol;mso-ansi-language:EN-GB'><span style='mso-list: Ignore'>�<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span lang=EN-GB style='mso-ansi-language: EN-GB'>Your object is present all time story. Just follow it with your mouse. When the stack is over you can add a new track pressing on  Add track .<o:p></o:p></span></p> <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space: auto;text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span lang=EN-GB style='font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol;mso-ansi-language:EN-GB'><span style='mso-list: Ignore'>�<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span lang=EN-GB style='mso-ansi-language: EN-GB'>Your object is present from the beginning to some middle time point. Follow your object with your mouse and when it disappears, click over the image with the middle button of your mouse (the wheel button). Then, press  End track . You can now add a new track pressing on  Add track .<o:p></o:p></span></p> <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space: auto;text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span lang=EN-GB style='font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol;mso-ansi-language:EN-GB'><span style='mso-list: Ignore'>�<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span lang=EN-GB style='mso-ansi-language: EN-GB'>Your object is present from some middle time point to another time point/end.<span style='mso-spacerun:yes'>� </span>Put your mouse over the image and when your object appears click over the image with the middle button of your mouse (the wheel button). Then, press F8 button from the keyboard to erase older positions tracked. It is important to have selected the image in order to do the delete. If you cannot see the list of tracks, press F5 button from the keyboard. When you are sure that older tracks positions have been deleted, click again over the image with the middle button to follow the tracking. If your object disappears before the end of the stack, click with the middle button of your mouse and the click  End track . In any case, press  Add track if you want to add a new track after this tracking.<o:p></o:p></span></p> <p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space: auto'><span lang=EN-GB style='mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'>To sum up:<o:p></o:p></span></p> <p class=MsoListParagraphCxSpFirst style='text-indent:-18.0pt;mso-list:l2 level1 lfo4'><![if !supportLists]><span lang=EN-GB style='font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol;mso-ansi-language:EN-GB'><span style='mso-list: Ignore'>�<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span lang=EN-GB style='mso-ansi-language: EN-GB'>Wheel button mouse. Stop/Resume tracking. You need to press this button if you want to click F8 or F5.<o:p></o:p></span></p> <p class=MsoListParagraphCxSpMiddle style='text-indent:-18.0pt;mso-list:l2 level1 lfo4'><![if !supportLists]><span lang=EN-GB style='font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol;mso-ansi-language:EN-GB'><span style='mso-list: Ignore'>�<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span lang=EN-GB style='mso-ansi-language: EN-GB'>F5: Show track list.<o:p></o:p></span></p> <p class=MsoListParagraphCxSpLast style='text-indent:-18.0pt;mso-list:l2 level1 lfo4'><![if !supportLists]><span lang=EN-GB style='font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol;mso-ansi-language:EN-GB'><span style='mso-list: Ignore'>�<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span lang=EN-GB style='mso-ansi-language: EN-GB'>F8: Erase older tracks from the current object.<o:p></o:p></span></p> <p class=MsoNormal style='tab-stops:874.0pt'><span lang=EN-GB style='mso-ansi-language:EN-GB'><span style='mso-tab-count:1'>�������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������� </span><o:p></o:p></span></p> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'>Figure 1:<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:70.8pt;text-indent:-70.8pt'><span lang=FR><!--[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="Imagen_x0020_1" o:spid="_x0000_s1026" type="#_x0000_t75" style='width:433.5pt;height:579.75pt;visibility:visible;mso-wrap-style:square; mso-left-percent:-10001;mso-top-percent:-10001;mso-position-horizontal:absolute; mso-position-horizontal-relative:char;mso-position-vertical:absolute; mso-position-vertical-relative:line;mso-left-percent:-10001; mso-top-percent:-10001'> <w:wrap type="none"/> <w:anchorlock/> </v:shape><![endif]--><![if !vml]><img width=578 height=773 src="figure1.png" v:shapes="Imagen_x0020_1"><![endif]></span><span lang=EN-GB style='mso-ansi-language:EN-GB'><o:p></o:p></span></p> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal><b><i><u><span lang=EN-GB style='mso-ansi-language:EN-GB'>Drawing:<o:p></o:p></span></u></i></b></p> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal><span lang=EN-GB style='mso-ansi-language:EN-GB'>In many cases, you will notice that in older Manual tracking versions when you press any button from drawing, <span class=SpellE>imageJ</span> (and probably your pc too) started to slow down its velocity and eventually it freezes. This is because when any of these buttons are pressed, <span class=SpellE>ImageJ</span> creates a new image that is stored in your RAM and sometimes this fills your entire RAM available. For example, a stack of 290 photos (1344x1024 px�) in 8-bit costs around 390 MB of RAM and if you press  Dots it will create you a new RGB image of 1.5 GB. In order to solve this problem now you can do:<o:p></o:p></span></p> <p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space: auto;text-indent:-18.0pt;mso-list:l1 level1 lfo6'><![if !supportLists]><span lang=EN-GB style='font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol;mso-ansi-language:EN-GB'><span style='mso-list: Ignore'>�<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span lang=EN-GB style='mso-ansi-language: EN-GB'>Create the same video but in 8-bit <span class=SpellE>color</span>. In this case, you have to activate  All same <span class=SpellE>color</span> . All dots/lines will be painted with the same <span class=SpellE>color</span> as the field next to  All same <span class=SpellE>color</span> and it must be a number between 0 (black) and 255 (white). In the previous example, the new video will cost ~390 MB in comparison to 1.5 GB.<o:p></o:p></span></p> <p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space: auto;text-indent:-18.0pt;mso-list:l1 level1 lfo6'><![if !supportLists]><span lang=EN-GB style='font-family:Symbol;mso-fareast-font-family:Symbol; mso-bidi-font-family:Symbol;mso-ansi-language:EN-GB'><span style='mso-list: Ignore'>�<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span lang=EN-GB style='mso-ansi-language: EN-GB'>Create only the first image. In this case, you have to activate  Only first . This option should be done with dots only. It will paint all first objects positions tracked either if its track start at frame 1 or in other frame. If  All same <span class=SpellE>color</span> is checked, the image created will be in black and white. Nevertheless, you could create it in <span class=SpellE>color</span> without fear because following with the <span class=GramE>example,</span> it would be ~ 5 MB.<o:p></o:p></span></p> </td> </tr> </table> <p><b><span lang=FR>|<a href="http://rsb.info.nih.gov/ij/plugins/index.html">Plugins</a>| <a href="http://rsb.info.nih.gov/ij/index.html">Home</a> |</span></b><span lang=FR> </span></p> <p class=MsoNormal><span lang=FR><o:p>&nbsp;</o:p></span></p> </div> </body> </html>