Recent changes to Advanced Tutorial

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 10:44:00 -0000

--- v27
+++ v28
@@ -97,3 +97,34 @@
 + Click on the [Show Paths](Images/attachment/path.png  "Show Paths") button and scroll through the movie. The [path](Images/attachment/advanced_tutorial_007.png "ROI Path") of the ROI up to the current frame is displayed on the Image Windows.
 + Click on the [No Paths](Images/attachment/no_path.png  "No Paths") button to hide the ROI path superimposed on the movie.
  
+[![Contents](http://sourceforge.net/p/cellsampler/wiki/Images/attachment/sec_bullet_up.gif "Contents")](#toc)
+
+###Sampling a Moving Feature (Shortcut Keys)###
+
+The functions of the [Nudge Control](#sampling-a-moving-feature) and the _Cell Sampler Window_ are also mapped to shortcuts accessed via the keyboard. By default these shortcut keys are inactive. The text below shows how to use the shortcut keys to re-position an ROI for sampling.
+
+1. With the example data set open, zoom in on the [2 top left features](Images/attachment/advanced_tutorial_002.png "Example Data Set") in the movie. 
++ Return the movie to frame 1 and click on the Add ROI On button. 
++ Click on the movie, placing a second ROI on the second feature. Click on the Add ROI Off button.
++ The second ROI is now the active ROI.
++ Click on the Show Cell Nudger button. When the Nudger Control is displayed, click on the Shorts On button. This will make the shortcuts active in the Image windows.
++ You will notice that the arrows of the Nudge Control are grayed out as the plugin is now expecting input for ROI positioning via the shortcut keys.
++ Click on the Hide Cell Nudger button to hide the Nudge Control.
++ Double click on a Image Window, switching the window focus to the movie images. If the window focus is not on the movie images, the shortcuts will not work.
++ Press the *W* key, this moves the active ROI up.
++ Press the *S* key, this moves the active ROI down.
++ Press the *A* key, this moves the active ROI to the left.
++ Press the *D* key, this moves the active ROI to the right.
++ W/S/A/D are referred as the direction shortcuts in the remainder of the document.
++ To move navigate through the frames of the video, use the _Left_ and _Right_ arrow keys.
++ Return the movie to frame 1.
++ Use the short direction shortcuts and the arrow keys to track the feature through the rest of the movie.
++ You will now have tracked 2 ROI features in the example data set.
++ To plot the time series of the active ROI, press *P* to plot the graph.
++ When plotting the graph, focus shifts to the graph window. Double click on the movie images to switch focus back to the Image Window.
++ Press *H* to display on the active.
+
+
+
+ 
+

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 09:17:14 -0000

--- v26
+++ v27
@@ -26,7 +26,7 @@
 
 ![Test Dataset](http://sourceforge.net/p/cellsampler/wiki/Images/attachment/fake_scn_0147.jpg "Test Data")
 
-_A single frame from the test data set showing 8 Regions-Of-Interest._
+_A single frame from the example data set showing 8 Regions-Of-Interest._
 
 [![Contents](http://sourceforge.net/p/cellsampler/wiki/Images/attachment/sec_bullet_up.gif "Contents")](#toc)

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 09:15:54 -0000

--- v25
+++ v26
@@ -84,7 +84,7 @@
 + Return the movie to frame 1.
 + Clicking on the [Add ROI On](Images/attachment/roi_on.png "Add ROI On") button.
 + Click on the feature in the movie that you wish to track, a [numbered ROI circle](Images/attachment/advanced_tutorial_003.png  "Image Window with ROI") will appear on both Image windows.
-+ Click on the [Show Plot](Images/attachment/plot.png "Show Plot") button to display the time series of the feature. This time series should be sinusoidally oscillating. As the feature is drifting however, the sampled drifts out of the ROI frame and the [time series](Images/attachment/advanced_tutorial_004.png "Time Series") is contains the random background pixel intensities.
++ Click on the [Show Plot](Images/attachment/plot.png "Show Plot") button to display the time series of the feature. This time series should be sinusoidally oscillating. As the feature is drifting the sampling fra,e (ROI) loses the feature and the [time series](Images/attachment/advanced_tutorial_004.png "Time Series") contains the random background pixel intensities from the later frames of the movie.
 + Return the movie to frame 1.
 + Click on the [Show Cell Nudger](Images/attachment/nudge.png "Show Cell Nudger") button to display the [Nudge Control](Images/attachment/advanced_tutorial_005.png "Nudge Control"). The [Nudge Control](Images/attachment/advanced_tutorial_005.png "Nudge Control") is used to re-position an ROI placed over a feature.
 + Click on the [green arrows](Images/attachment/advanced_tutorial_005.png "Nudge Control") to move the yellow ROI circle up/down/left/right. The aim is to position the circle over the feature being sampled.

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 08:54:32 -0000

--- v24
+++ v25
@@ -84,8 +84,7 @@
 + Return the movie to frame 1.
 + Clicking on the [Add ROI On](Images/attachment/roi_on.png "Add ROI On") button.
 + Click on the feature in the movie that you wish to track, a [numbered ROI circle](Images/attachment/advanced_tutorial_003.png  "Image Window with ROI") will appear on both Image windows.
-+ Click on the [Show Plot](Images/attachment/plot.png  "Show Plot") button to display the time series of the feature.
-+ This time series should be sinusoidally oscillating. As the feature is drifting however, the [time series](Images/attachment/advanced_tutorial_004.png "Time Series") is measuring random background pixel intensities.
++ Click on the [Show Plot](Images/attachment/plot.png "Show Plot") button to display the time series of the feature. This time series should be sinusoidally oscillating. As the feature is drifting however, the sampled drifts out of the ROI frame and the [time series](Images/attachment/advanced_tutorial_004.png "Time Series") is contains the random background pixel intensities.
 + Return the movie to frame 1.
 + Click on the [Show Cell Nudger](Images/attachment/nudge.png "Show Cell Nudger") button to display the [Nudge Control](Images/attachment/advanced_tutorial_005.png "Nudge Control"). The [Nudge Control](Images/attachment/advanced_tutorial_005.png "Nudge Control") is used to re-position an ROI placed over a feature.
 + Click on the [green arrows](Images/attachment/advanced_tutorial_005.png "Nudge Control") to move the yellow ROI circle up/down/left/right. The aim is to position the circle over the feature being sampled.

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 08:42:55 -0000

--- v23
+++ v24
@@ -77,7 +77,7 @@
 
 [![Contents](http://sourceforge.net/p/cellsampler/wiki/Images/attachment/sec_bullet_up.gif "Contents")](#toc)
 
-###Placing a ROI over a moving Feature###
+###Sampling a Moving Feature (Nudge Control)###
 
 1. With the example data set open, zoom in on the [2 top left features](Images/attachment/advanced_tutorial_002.png "Example Data Set") in the movie.
 + Scroll through the image and note that these features drift during the movie.

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 08:41:28 -0000

--- v22
+++ v23
@@ -11,7 +11,7 @@
 
 ###Prerequisites###
 
-* Install the _Cell-Sampler/ImageJ_ bundle (see [Installation]).
+* Install the _Cell Sampler/ImageJ_ bundle (see [Installation]).
 * Read the [Basic Tutorial].
 * [Download Example Dataset](http://sourceforge.net/projects/cellsampler/files/test_data2.zip).

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 08:23:15 -0000

--- v21
+++ v22
@@ -96,5 +96,5 @@
 + Scroll through the movie, you will see the ROI circle move between frames.
 + Return the movie to frame 1.
 + Click on the [Show Paths](Images/attachment/path.png  "Show Paths") button and scroll through the movie. The [path](Images/attachment/advanced_tutorial_007.png "ROI Path") of the ROI up to the current frame is displayed on the Image Windows.
-+ Click on the [No Paths](Images/attachment/path.png  "No Paths") button to hide the ROI path superimposed on the movie.
++ Click on the [No Paths](Images/attachment/no_path.png  "No Paths") button to hide the ROI path superimposed on the movie.

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 08:18:10 -0000

--- v20
+++ v21
@@ -79,24 +79,22 @@
 
 ###Placing a ROI over a moving Feature###
 
-1. With the example data set open, zoom in on the [2 top left](Images/attachment/advanced_tutorial_002.png "Example Data Set") features in the movie.
+1. With the example data set open, zoom in on the [2 top left features](Images/attachment/advanced_tutorial_002.png "Example Data Set") in the movie.
 + Scroll through the image and note that these features drift during the movie.
 + Return the movie to frame 1.
-+ Place a ROI over the top left feature, clicking on the ROI button and then on feature.
-+ A number ROI circle will appears on both Image windows.
-+ Click on the Show Plot button to display the time series of the feature.
-+ This time series should be sinusoidally oscillating, however as the feature is drifting the ROI placed over the feature is not tracking the feature's path.
++ Clicking on the [Add ROI On](Images/attachment/roi_on.png "Add ROI On") button.
++ Click on the feature in the movie that you wish to track, a [numbered ROI circle](Images/attachment/advanced_tutorial_003.png  "Image Window with ROI") will appear on both Image windows.
++ Click on the [Show Plot](Images/attachment/plot.png  "Show Plot") button to display the time series of the feature.
++ This time series should be sinusoidally oscillating. As the feature is drifting however, the [time series](Images/attachment/advanced_tutorial_004.png "Time Series") is measuring random background pixel intensities.
 + Return the movie to frame 1.
-+ Click on the Show Cell Nudger button to display the Nudge Control
-+ Click on the green arrows to move the yellow ROI circle up/down/left/right. The aim is to position the circle over the feature being sampled.
-+ Click on the black arrow to move, the next frame and adjust the ROI position over the feature.
++ Click on the [Show Cell Nudger](Images/attachment/nudge.png "Show Cell Nudger") button to display the [Nudge Control](Images/attachment/advanced_tutorial_005.png "Nudge Control"). The [Nudge Control](Images/attachment/advanced_tutorial_005.png "Nudge Control") is used to re-position an ROI placed over a feature.
++ Click on the [green arrows](Images/attachment/advanced_tutorial_005.png "Nudge Control") to move the yellow ROI circle up/down/left/right. The aim is to position the circle over the feature being sampled.
++ Click on the [black arrows](Images/attachment/advanced_tutorial_005.png "Nudge Control") to move, the next frame and adjust the ROI position over the feature.
 + Continue tracking the features path until the end of the movie.
-+ Click on the Show Cell Nudger.
-+ Click on the Show Plot button to display the time series of the feature. It now shows a noisy sinusoidal trace.
++ Click on the [Hide Cell Nudger](Images/attachment/no_nudge.png "Hide Cell Nudger") to close the _Nudge Control_.
++ Click on the [Hide Plot](Images/attachment/no_plot.png  "Hide Plot") and [Show Plot](Images/attachment/plot.png  "Show Plot") buttons to re-plot the time series. It now shows a [noisy sinusoidal trace](Images/attachment/advanced_tutorial_006.png "noisy sinusoidal trace") as the ROI is tracking the feature movement.
 + Scroll through the movie, you will see the ROI circle move between frames.
 + Return the movie to frame 1.
-+ Click on the Show Paths button and scroll through the movie. The path of the ROI up to the current frame is shown on the Image Windows.
-+ Click on the No Paths buttons to hide the ROI path superimposed on the movie.
-
-
++ Click on the [Show Paths](Images/attachment/path.png  "Show Paths") button and scroll through the movie. The [path](Images/attachment/advanced_tutorial_007.png "ROI Path") of the ROI up to the current frame is displayed on the Image Windows.
++ Click on the [No Paths](Images/attachment/path.png  "No Paths") button to hide the ROI path superimposed on the movie.

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 07:27:28 -0000

--- v19
+++ v20
@@ -79,7 +79,7 @@
 
 ###Placing a ROI over a moving Feature###
 
-1. With the example data set open, zoom in on the [2 top left](Images/attachmentadvanced_tutorial_002.png "Example Data Set") features in the movie.
+1. With the example data set open, zoom in on the [2 top left](Images/attachment/advanced_tutorial_002.png "Example Data Set") features in the movie.
 + Scroll through the image and note that these features drift during the movie.
 + Return the movie to frame 1.
 + Place a ROI over the top left feature, clicking on the ROI button and then on feature.

WikiPage Advanced Tutorial modified by Gareth Smith

Gareth Smith — Fri, 17 Aug 2012 07:26:53 -0000

--- v18
+++ v19
@@ -79,7 +79,7 @@
 
 ###Placing a ROI over a moving Feature###
 
-1. With the example data set open, zoom in on the 2 top left feature in the example data set.
+1. With the example data set open, zoom in on the [2 top left](Images/attachmentadvanced_tutorial_002.png "Example Data Set") features in the movie.
 + Scroll through the image and note that these features drift during the movie.
 + Return the movie to frame 1.
 + Place a ROI over the top left feature, clicking on the ROI button and then on feature.
@@ -96,7 +96,7 @@
 + Scroll through the movie, you will see the ROI circle move between frames.
 + Return the movie to frame 1.
 + Click on the Show Paths button and scroll through the movie. The path of the ROI up to the current frame is shown on the Image Windows.
-+ 
++ Click on the No Paths buttons to hide the ROI path superimposed on the movie.