https://sourceforge.net/p/cellsampler/wiki/Tutorials/Recent changes to TutorialsenTue, 13 Sep 2016 10:45:25 -0000https://sourceforge.net/p/cellsampler/wiki/Tutorials/<div class="markdown_content"><pre></pre> </div>Gareth SmithTue, 13 Sep 2016 10:45:25 -0000https://sourceforge.net3f9af484bfd3c3617838ae0530342e51fb817b49https://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre></pre>Gareth SmithFri, 17 Aug 2012 08:36:41 -0000https://sourceforge.net944731fcaa4c88d038d6bf08aaf499f735524701https://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre>--- v98 +++ v99 @@ -8,7 +8,7 @@ --- ###Description### -This document contains links to two short tutorials on how to use the _Cell-Sampler_ plugin to obtain time series from microscope TIFF movies expressing the GFP or luciferase reporter molecules. +This document contains links to two short tutorials on how to use the _Cell Sampler_ plugin to obtain time series from microscope TIFF movies expressing the GFP or luciferase reporter molecules. [-&gt; Tutorial Material](#tutorial-material) @@ -19,7 +19,7 @@ The sampling processing to get time series from a TIFF movie consists of the following basic steps. Each of these basic steps is described in the [Tutorial Material](#tutorial-material). -1. Starting ImageJ and the Cell Sampler plugin. +1. Starting _ImageJ_ and the _Cell Sampler_ plugin. + Opening the Image Stack in the plugin. + Placement of ROI on the images, specifying the sampling coordinates for cellular features in a movie. + Saving the sampled ROI coordinates to file. @@ -29,7 +29,7 @@ ###Working Directories### -When working with imaging data, it is recommended that you keep your _imaging data files_ and output files from _Cell-Sampler_ in their own directories. This keeps the plugin's inputs and outputs separate. For each TIFF movie sampled by this plugin, try to create an output directory for the set of output files created by the plugin. +When working with imaging data, it is recommended that you keep your _imaging data files_ and output files from _Cell Sampler_ in their own directories. This keeps the plugin's inputs and outputs separate. For each TIFF movie sampled by this plugin, try to create an output directory for the set of output files created by the plugin. [](#toc) </pre>Gareth SmithFri, 17 Aug 2012 08:35:34 -0000https://sourceforge.net42b767d63a53465b1cc676a89efba2eb3b1dc4abhttps://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre></pre>Gareth SmithThu, 16 Aug 2012 09:17:28 -0000https://sourceforge.net52deee0f44f58aa3f250be97cf4c280c97b1cd99https://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre>--- v96 +++ v97 @@ -17,7 +17,7 @@ ###Overview of the Sampling Process### The sampling processing to get time series from a TIFF movie consists of the following basic steps. -Each of these steps is described in the later sections. +Each of these basic steps is described in the [Tutorial Material](#tutorial-material). 1. Starting ImageJ and the Cell Sampler plugin. + Opening the Image Stack in the plugin. </pre>Gareth SmithThu, 16 Aug 2012 09:13:29 -0000https://sourceforge.net6ebae17043093fd3f9d62fe24de77be96a912568https://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre>--- v95 +++ v96 @@ -40,6 +40,6 @@ Title | Description ------|------------ [Basic Tutorial] | Reviews how to open TIFF movies and position Regions-Of-Interest (ROI) for sampling. -[Advanced Tutorial] | Review how to use the plugin to track cellular drift in a movie. +[Advanced Tutorial] | Reviews how to use the plugin to track cellular drift in a movie. [](#toc) </pre>Gareth SmithThu, 16 Aug 2012 08:56:08 -0000https://sourceforge.netdadc840081f039369c5ce74193da1f22b553a22ahttps://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre>--- v94 +++ v95 @@ -6,35 +6,15 @@ [TOC] --- -##Description## +###Description### -This document contains two short tutorials on how to use the Cell-Sampler plugin to obtain time series from microscope TIFF movies expressing the GFP or luciferase reporter molecules. -The [Basic Tutorial](#basic-tutorial) describes how to open TIFF movies and position Regions-Of-Interest (ROI) for sampling. -The [Advanced Tutorial](#advanced-tutorial) describes how to use the plugin to track cellular drift in a movie. +This document contains links to two short tutorials on how to use the _Cell-Sampler_ plugin to obtain time series from microscope TIFF movies expressing the GFP or luciferase reporter molecules. +[-&gt; Tutorial Material](#tutorial-material) + [](#toc) ---- -##Prerequisites## - -* Install the _Cell-Sampler/ImageJ_ bundle (see [Installation]). -* [Basic Tutorial Dataset](http://sourceforge.net/projects/cellsampler/files/test_data1.zip). -* [Basic Tutorial Overlay File](http://sourceforge.net/projects/cellsampler/files/test_data1.csv). -* [Advanced Tutorial Dataset](http://sourceforge.net/projects/cellsampler/files/test_data2.zip). - -[](#toc) - ---- - -##Working Directories## - -When working with imaging data, it is recommended that you keep your _imaging data files_ and output files from _Cell-Sampler_ in their own directories. This keeps the plugin's inputs and outputs separate. For each TIFF movie sampled by this plugin, try to create an output directory for the set of output files created by the plugin. - -[](#toc) - ---- - -##Overview of the Sampling Process## +###Overview of the Sampling Process### The sampling processing to get time series from a TIFF movie consists of the following basic steps. Each of these steps is described in the later sections. @@ -47,26 +27,19 @@ [](#toc) ---- +###Working Directories### -##Advanced Tutorial## - -###Example Dataset### - -*[Download](http://sourceforge.net/projects/cellsampler/files/test_data2.zip)* - -The _example data set_ consists of a TIFF movie. -This movie has 172 _noisy_ frames (512x512 px), each frame contains 8 fuzzy Regions-Of-Interest (ROI) whose intensity varies sinusoidally overtime. Each feature represents a cell and is ~6 pixels in diameter. Each frame is placed in a unique file ordered numerically by file name. An example of a frame from this example data set is shown below. Each _feature_ in the movie performs a random-walk every other frame, moving towards the outer edge of the movie. This example data set was created with ImageJ. - - - -_A single frame from the test data set showing 8 Regions-Of-Interest._ +When working with imaging data, it is recommended that you keep your _imaging data files_ and output files from _Cell-Sampler_ in their own directories. This keeps the plugin's inputs and outputs separate. For each TIFF movie sampled by this plugin, try to create an output directory for the set of output files created by the plugin. [](#toc) -###Tracking Cell Drift### +--- -1. *[Download](http://sourceforge.net/projects/cellsampler/files/test_data2.zip)* the example dataset for this tutorial. Unzip the archive and place the images somewhere you can find them. -+ Create an directory to store output files created by the plugin. -+ Start ImageJ and from the ImageJ main menu, select _Plugins->Cell Sampler_. -+ Wait for the 2 images... +###Tutorial Material### + +Title | Description +------|------------ +[Basic Tutorial] | Reviews how to open TIFF movies and position Regions-Of-Interest (ROI) for sampling. +[Advanced Tutorial] | Review how to use the plugin to track cellular drift in a movie. + +[](#toc) </pre>Gareth SmithThu, 16 Aug 2012 08:55:23 -0000https://sourceforge.net0b8d4cc0008c4a62464054e7327cb66d026f7cefhttps://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre>--- v93 +++ v94 @@ -1,4 +1,5 @@ -#_Cell-Sampler:_ Tutorials# +#Cell Sampler# +##Tutorials## --- <a id="toc"></a> </pre>Gareth SmithThu, 16 Aug 2012 08:34:48 -0000https://sourceforge.net78fbb9f431beb2a4684c2f58875ccd9c8e105088https://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre>--- v92 +++ v93 @@ -48,262 +48,6 @@ --- -##Basic Tutorial## - -###Example Dataset### - -*[Download](http://sourceforge.net/projects/cellsampler/files/test_data1.zip)* - -The _example data-set_ consists of a TIFF movie. -This movie has 172 _noisy_ frames (110x162 px), each frame contains 6 bright Regions-Of-Interest (ROI) whose intensity varies sinusoidally overtime. Each bright region represents a cell-like feature. Each frame is placed in a unique file ordered numerically by file name. An example of a frame from this example data-set is shown below. This example data-set was created with ImageJ. - - - -_A single frame from the test data set showing 6 bright Regions-Of-Interest._ - -[](#toc) - -###Display Modes### - -The plugin can be started in 3 modes called _Cell Sampler_, _Cell Sampler Lazy_ and _Cell Sampler Mono_. These modes relate to how the software opens and displays the imaging data. If the plugin is started with _Cell Sampler_ or _Cell Sampler Lazy_, the imaging data is displayed in 2 windows. These windows are labeled _Raw_ and _Processed_. Imaging data is always sampled from the _Raw_ window. The _Processed_ window allows filters to be applied to a movie to segment a cellular feature against the background. Navigation and _user_ interaction between the 2 windows is linked. Applying a filter to the processed window is demonstrated in this [screen shot](Images/attachment/Screen-shot.jpg "Screen Shot") of the plugin. The greyscale TIFF movie is display in the left _Raw_ Image window. The right _Processed_ window was smoothed and a colour table applied to the imaging data to find areas of high pixel intensity (i.e. cellular features). _Cell Sampler Mono_ opens a TIFF movie a single window titled _Raw_. - -If you require two linked _Image Windows_ and the TIFF movie is large, it is recommended to start the plugin using _Cell Sampler Lazy_. This option opens a movie as a virtual stack, thereby reducing the memory needed to display an image for a small drop in performance. - -[](#toc) - -###Starting the Plugin and Opening a TIFF Movie### - -_N/B Only one instance of the Cell-Sampler plugin can run within ImageJ._ - - -1. *[Download](http://sourceforge.net/projects/cellsampler/files/test_data1.zip)* and unzip the example data set for this tutorial. -+ Create an directory to store output files created by the plugin. -+ Start ImageJ. If using a Mac click on _ImageJ.app_ or if on a PC, click on _ImageJ.exe_. These files are found in the root directory of the software. -+ From the Main menu of ImageJ, select _Plugins->Cell Sampler_. -+ A [Start Window](Images/attachment/basic_tutorial_001.png "Start Window") appears containing 2 buttons. Without clicking, hover your mice over the left button. A message will appear saying _Open TIFF Directory_. -+ Click on the left button to open a File Dialog window. -+ Choose the directory where your TIFF images are located. For this tutorial, select the directory _test_data1_, which contains the example images. -+ Press the _Choose_ button to select that directory. -+ If you press _Cancel_ or the selected directory contains no TIFF images, you will get a warning message. -+ The plugin will load TIFF movie, opening 3 windows. Two of the windows will be standard ImageJ image windows. The third window is the [Cell Sampler Window](Images/attachment/basic_tutorial_002.png "Cell Sampler Window"). -+ By default, all of the windows will be centrally positioned onscreen. Arrange the window so that you can see all the windows. When zooming an image, ImageJ will enlarge the display window. Position the imaging windows so your view is not obscured while zooming. This principle is shown by the 2 images below. - -[Image:](Images/attachment/basic_tutorial_003.png "Example Image") _Cell-Sampler plugin with 2-opened imaging windows, centrally positioned to permit zooming._ - -[Image:](Images/attachment/basic_tutorial_004.png "Example Image") _Cell-Sampler plugin with 2-opened imaging windows, images magnified by 200%._ - -_N/B Sometimes ImageJ will hang when trying to load images. If this occurs you may have too many applications open and ImageJ has not enough memory to open a movie. When using ImageJ, close as many superfluous applications as possible so that ImageJ will run with the optimum performance._ - -[](#toc) - -###Exiting the Plugin### - -* The plugin opens several windows within ImageJ. -* The management of these windows is controlled by the plugin, rather than ImageJ. -* To close these windows, select the File->Exit option in the [Cell Sampler Window](Images/attachment/basic_tutorial_009.png "Cell Sampler Window"). -* If you have positioned ROI on a movie, the plugin will ask to _Save the Sampled ROI_ before exiting. -* If you try to close an opened window without _Exiting_ from the [Cell Sampler Window](Images/attachment/basic_tutorial_009.png "Cell Sampler Window"), the plugin will display a warning message. -* If filters were applied to the TIFF movie to enhance the imaging data, when closing the plugin will never attempt to save the modified file. - -[](#toc) - -###Zooming, Frame Navigation and the Default View### - -_N/B Slice = Movie Frame_ - -If the plugin is closed, open the plugin as described in [Starting the Plugin and Opening a TIFF Movie](#Starting-the-Plugin-and-Opening-a-TIFF-Movie). - -1. When the plugin starts initially, _zooming_ is switched on and linked to mouse click on a image. Click on the 'Raw' image window twice in the top left corner of that window. This will perform a 200% zoom in both imaging windows. -+ Zooming can be toggled off or on by clicking on the [Zoom On](Images/attachment/zoom_on.png "Zoom On") or [Zoom Off](Images/attachment/zoom_off.png "Zoom Off") buttons. -+ Click on the [Cell Sampler Window](Images/attachment/basic_tutorial_002.png "Cell Sampler Window") and use the horizontal scrollbar to move through the movie. For more accurate navigation, use the arrows on the scrollbar. You will see both image windows scroll through the movie frames. -+ Move the scrollbar to navigate to the middle on the movie. -+ To return to Frame 1 you can use the scrollbar or the [Default View](Images/attachment/default.png "Default View Button") button. -+ Initially clicking on [Default View](Images/attachment/default.png "Default View Button") button does nothing. The navigation option of this button need to be enabled. -+ To enable the [Default View](Images/attachment/default.png "Default View Button") button, click on the [Settings Button](Images/attachment/settings.png "Settings Button") to display the [Settings Window](Images/attachment/basic_tutorial_005.png "Settings Window"). -+ Check the options _Go to Slice 1 on Default View_ and _Unzoom on ROI navigation_ and click on the _Ok_ button. -+ Click on "Default View Button", the Image windows will return to Frame 1 and the default aspect ratio (unzoom) when the movie was initially opened. - -[](#toc) - -###Placing a Region-of-Interest (ROI) for Sampling### - -Placing a ROI means that you have found a _cellular feature_ that you wish to track and sample. -Sampling collects 2 sets of information about a ROI, the average pixel intensity in the ROI and the ROI position per frame in the movie. -ROI used by this plugin are all circular in shape. - -_N/B ROI position and size can be modified after initial placement._ - -1. Before placing ROI on a image, inspect the Image data and assess how big the default ROI needs to be when placed over a cell. The default diameter of a cell is assumed to be 6 pixels. -+ To change the default ROI size, click on the [Settings Button](Images/attachment/settings.png "Settings Button") to display the [Settings Window](Images/attachment/basic_tutorial_005.png "Settings Window"). -+ Select an appropriate value from the _Default ROI Size (px)_ option and click _Ok_. Default size can range from 3-12 pixels. For the best placement of a ROI, an even-numbered size is recommended as ROI are placed relative to the pixel grid of a image. -+ Click on the [Zoom On](Images/attachment/zoom_on.png "Zoom On") button to activate the zoom function. -+ Click on the processed window twice to do a 200% magnification of the Image. -+ Click on the [Add ROI On](Images/attachment/basic_tutorial_005.png "Add ROI On") button (green circle) to switch on the _Add ROI_ option. You will notice that the zooming option is now inactive. -+ Place focus on the _Processed_ image window by clicking once on the window title. -+ Slowly move the mouse cursor onto the image surface and in the middle of topmost bright most bright region. -+ Click once with your mouse, a ROI is placed on the plotting surface. This region is labelled as _ 1 _. Each ROI added to an image is given a unique, sequential, integer identifier. -+ When a ROI is placed on one image window, it is immediately echoed in the second. There is a 1 second delay between ROI placement. -+ Place a ROI each of the bright regions of the image. The display of the Raw Window should look similar to this [image](Images/attachment/basic_tutorial_006.png "ROI Placement"). - -[](#toc) - -###Saving the ROI Coordinates to File### - -This software does not provide an _Undo_ option. -It is recommended that you have your work periodically. -If you close and exit the plugin, you will be prompted if you wish to save your work. - -To save the ROI coordinates to file, do the following. - -1. This software will only save ROI coordinates if ROI are placed on a movie. -+ Place ROI on the TIFF movie and create (if necessary) an output directory for files generated by this plugin. -+ In the [Cell Sampler Window](Images/attachment/basic_tutorial_009.png "Cell Sampler Window"), select the _File->Save ROI_ option from the menu. -+ A File dialogue appears asking to you to _Select XML File for ROI_. -+ Use the file dialogue to navigate to your output directory. -+ The output file name is preset, using the directory name where the imaging data is stored as the default file stem. You can specify your own file name. -+ If you have used example dataset, the XML file is called _test_data1.xml_. -+ Click on the _Save_ button to save your work to file. If you press _Cancel_, the plugin displays a warning message. -+ ROI coordinates/types/export status, colour selections, default ROI size and paths to the source images are written to file. The XML is a text file format and so saved file can be opened with any standard text editor. -+ If normally takes just a couple of second to save the file. A dialogue will appear when the save has completed. - -[](#toc) - -###Opening the ROI Coordinates File### - -To open an existing XML file created by the _Cell-Sampler_ plugin, specifying the position of ROI in a TIFF movie, do the following. - -1. If the Cell-Sampler plugin is open, close the plugin as described in [Exiting the Plugin](#Exiting-the-Plugin###). -+ Start ImageJ and from the main menu, select _File->Plugins->Cell Sampler_ option. -+ The [Start Window](Images/attachment/basic_tutorial_001.png "Start Window") appears containing 2 buttons. Without clicking, hover your mice over the right button. A message will appear saying _Open Saved ROI XML File_. -+ Use the File Dialogue to select a XML file created by the _Cell-Sampler_ plugin. -+ Click _Open_ to load the TIFF images and the ROI coordinates data. -+ If _Cancel_ is pressed, the plugin will display a warning message. - -[](#toc) - -###ROI Navigation### - -For each ROI placed on a image, a number of operations can be performed on a ROI such as plotting the time series or re-positioning the ROI in a frame of the movie. -These operations are performed on the active ROI id. -The currently active ROI id and its coordinates in frame 1 of a movie are displayed in the [Cell Sampler Window](Images/attachment/basic_tutorial_007.png "Active ROI"). This plugin provides a number of options to navigate around the ROI placed on a movie. - -1. Click on the [Hide ROI](Images/attachment/hide.png "Hide ROI") button. This option leaves only the active ROI in the Image Window. -+ Click on the [Show ROI](Images/attachment/show.png "Show ROI") button to redisplay all of the ROI in the Image Windows. -+ To move through the ROI list, use the _black_ navigation arrows on the [Cell Sampler Window](Images/attachment/basic_tutorial_007.png "Cell Sampler Window"). ROI navigation is circular. -+ Click on the navigation arrows to move through the ROI list. -+ If the appropriate settings are specified, the Image Windows Try this with [ROI Hidden](Images/attachment/hide.png "ROI Hidden") and [ROI Shown](Images/attachment/hide.png "ROI Shown"). If the option is specified in the Settings Window, ROI navigation will unzoom the image window(s) and reset the movie back to Frame 1. -+ Click on the [Go to ROI](Images/attachment/jump.png "Go to ROI") button and enter a ROI id. Click _Ok_ to the active ROI. This option is useful if you do not wish to scroll through a lengthy list. - -[](#toc) - -###ROI Deletion### - -1. To delete a ROI placed on a movie, use the navigation controls to set the ROI as the active ROI. -+ Click on the [Delete ROI](Images/attachment/delete.png "Delete ROI") button. -+ The ROI is deleted. Be warned that there is no Undo option in this software. -+ When a ROI is deleted, the active ROI becomes the previous ROI in the list. - -[](#toc) - -###Plotting the Time Series### -1. To plot the time series associated with a ROI, use the navigation controls to set the ROI as the active ROI. -+ Click on the [Show Plot](Images/attachment/plot.png "Show Plot") button to display a graph. The graph window is resizable. -+ Moving the mouse cursor over the graph surface will display the _time index_ and _intensity value_. -+ Clicking on the graph surface at a specific time index will cause to Image window(s) to display that frame from the source movie. -+ When a plot is showing, click on the [Hide Plot](Images/attachment/no_plot.png "Hide Plot") button to close the graph. -+ If ROI position is modified, the graph is not automatically updated. To re-plot a graph click the [Hide Plot](Images/attachment/no_plot.png "Hide Plot") and [Show Plot](Images/attachment/plot.png "Show Plot") buttons. -+ The active ROI can be reset via the navigation controls. If a graph is displayed whilst changing the active ROI, the plot updates automatically. - -[](#toc) - -###Specifying a ROI for Export### - -1. To specify that a ROI is for export, set the appropriate Keep? flag on the [Cell Sampler Window](Images/attachment/basic_tutorial_002.png "Cell Sampler Window"). -+ By default, all ROI placed on a movie are flagged for export. -+ Setting Keep? to _No_ means that the ROI in the Image Window(s) is coloured _black_. -+ Setting Keep? to _Maybe_ means that the ROI in the Image Window(s) is coloured _blue_. -+ Setting Keep? to _No_ means that the ROI time series is never exported into final dataset created by the plugin. -+ When changing the Keep? state of a ROI, the running total of ROI to be included in the exported dataset is echoed in the [Cell Sampler Window](Images/attachment/basic_tutorial_008.png "Cell Sampler Window"). - -[](#toc) - -###Setting ROI Type### - -1. Each ROI placed on a movie can be assigned a _type_, i.e. a broad classification of the cellular feature based on position or time series topology. -+ The default value for type is _Unspecified_. -+ The list of available types is found in the file _~/plugins/Cell_Types.csv_ located in the ImageJ installation root directory. -+ This file must be present and have at least one category defined otherwise the plugin will not work. -+ To specify your own type categories, update the the category list contained in this file. -+ The default type (_e.g._ Unspecified) is always the first in the list located in _~/plugins/Cell_Types.csv_. - -[](#toc) - -###Feature Overlay File### - -The plugin can load and display coordinates from an overlay file. An overlay file consists of a text CSV file containing 2 columns of numbers. The numbers are the cartesian coordinates (x,y) of a features found in the first frame of a TIFF movie. - -To use a overlay file with this tutorial's example data-set, do the following:- - -1. Download the [Example Overlay File](http://sourceforge.net/projects/cellsampler/files/test_data1_overlay.csv "Example Overlay File") and place this file in your output directory. -+ Start ImageJ and either load the example data-set or load the saved ROI XML file. -+ Click on the [Show Overlay](Images/attachment/overlay.png "Show Overlay"), a file dialogue window will appear. -+ Select the overlay file and click _Open_. If you press _Cancel_ the plugin will report an error. -+ Circles will appear, showing the position of flagged features. -+ Unlike manually placed ROI, overlay features are not numbered. -+ The display of the overlay can be toggled off or on by using the [Show Overlay](Images/attachment/overlay.png "Show Overlay") / [No Overlay](Images/attachment/no_overlay.png "No Overlay") buttons. -+ [Image](Images/attachment/basic_tutorial_010.png "Image"): Overlay file displayed by the plugin is shown. Red circles use coordinates from the overlay file, numbered yellow circles are manually placed ROI. -+ The colour and size of the overlay can be modified by using the _Overlay Colour_ and _Default ROI Size_ options in the [Settings Window](Images/attachment/basic_tutorial_005.png "Settings Window"). -+ Click on the the [Settings Button](Images/attachment/settings.png "Settings Button") to show the [Settings Window](Images/attachment/basic_tutorial_005.png "Settings Window"). - -[](#toc) - -###Exporting Time Series### - -To export the time series obtained from a movie to file, do the following:- - -1. In the [Cell Sampler Window](Images/attachment/basic_tutorial_009.png "Cell Sampler Window"), select the _File->Export Time Series_ option from the menu. If the movie has no ROI, the plugin will flag an error. -+ A file dialogue appears stating to _Choose a Directory for Time Series_. The plugin creates several files when exporting time series, hence it asks for a directory. -+ Click _Choose_ to start the export. If _Cancel_ is pressed, the plugin will display an error. -+ For a large movie with many sampled ROI, it can take up to 30 seconds to generate the output files. The progress bar on the bottom of the [Cell Sampler Window](Images/attachment/basic_tutorial_005.png "Cell Sampler Window") can be used to follow the status of the export. -+ An dialogue window will appear when the export is complete. -+ The _shared_ file stem of the generated files is set by the file name used to save the ROI XML file (see _[Saving The ROI Coordinates to File](#saving-the-roi-coordinates-to-file)_). - -The exported time series files for this tutorial are found *[here](http://sourceforge.net/projects/cellsampler/files/test_data1_export.zip)*. - -A list of the output files containing the time series and positional information derived from the example data-set (_test_data1_) is listed below. - -Output File | Contents -------------|--------- -test_data1.xml | The XML file containing the sampling ROI manually set by a user using the _Cell-Sampler_ plugin. -test_data1_intensities.csv | Column-major spreadsheet containing time series derived from the imaging data. First row of spread is Cell Identifiers. Second row of spreadsheet is the specified cell type. Third row of spreadsheet is the cell position at frame 1 of a movie. The remaining rows is the time series data. -test_data1_intensities2.csv | Row-major spreadsheet containing only time series derived from the imaging data. Time series related to positional information by index number. -test_data1_dim.csv | The dimension of the exported time series (No. Exported cell x No. Frames). -test_data1_mask.csv | A binary masking file to differentiate cells flagged as 'Yes' or 'Maybe'. -test_data1_id.csv | A list of ROI numerical identifiers exported. Identifiers related to time series/positional data by index number -test_data1_xy.csv | The positional information of each tracked ROI in a movie. Used to record cell movement. -test_data1_averages.csv | Average background image intensities of each frame in a movie - -[](#toc) - -###Copying Projects between Computers### - -The _Cell-Sampler_ plugin is cross-platform as the _plugin/ImageJ_ software bundle will run on both _Mac_ and _Windows_ computers. -A XML file of ROI coordinates (_i.e. a project_) created by the plugin is transferable between different computers. - -To copy a project between different computers, do the following:- - -1. Copy the imaging data between the 2 computers and take note of the path of the destination directory. If the plugin cannot load the TIFF images of a movie when it opens a _project_ XML file, it will report an error. -+ Update the path to the source images in the ROI XML, do this by editing the XML file created by the plugin. -+ Open the XML file in a text editor (_e.g._ Notepad/TextEdit). -+ Update the image path within the _directory_ tags with the _new_ directory path on the destination computer. An example of the directory tag is shown below. When updating the directory path, its safest to forward slash "/" when specifying the delimiting the path components. Always specify the _absolute_ path a the image directory. -+ To find the directory tag in the XML document, use the text editor search function (_e.g._ Ctrl+f) or scroll down to the bottom of the XML document. - -&lt;directory&gt;/Users/auser/Images/SCN Slice-1&lt;/directory&gt; - -[](#toc) - ---- - ##Advanced Tutorial## ###Example Dataset### </pre>Gareth SmithThu, 16 Aug 2012 08:16:00 -0000https://sourceforge.net02070bd95c5cb338b2558298d4994860df841ce8https://sourceforge.net/p/cellsampler/wiki/Tutorials/<pre>--- v91 +++ v92 @@ -270,7 +270,7 @@ The exported time series files for this tutorial are found *[here](http://sourceforge.net/projects/cellsampler/files/test_data1_export.zip)*. -The list of the output file containing the time series and postional information derived from the example data-set (_test_data1_) is listed below. +A list of the output files containing the time series and positional information derived from the example data-set (_test_data1_) is listed below. Output File | Contents ------------|--------- @@ -311,10 +311,17 @@ *[Download](http://sourceforge.net/projects/cellsampler/files/test_data2.zip)* The _example data set_ consists of a TIFF movie. -This movie has 172 _noisy_ frames (512x512 px), each frame contains 8 fuzzy Regions-Of-Interest (ROI) whose intensity varies sinusoidally overtime. Each feature represents a cell and is approximately 6 pixels in diameter. Each frame is placed in a unique file ordered numerically by file name. An example of a frame from this example data set is shown below. Each _cell_ in the movie performs a random-walk every other frame, moving towards the outer edge of the image. This example data set was created with ImageJ. +This movie has 172 _noisy_ frames (512x512 px), each frame contains 8 fuzzy Regions-Of-Interest (ROI) whose intensity varies sinusoidally overtime. Each feature represents a cell and is ~6 pixels in diameter. Each frame is placed in a unique file ordered numerically by file name. An example of a frame from this example data set is shown below. Each _feature_ in the movie performs a random-walk every other frame, moving towards the outer edge of the movie. This example data set was created with ImageJ.  _A single frame from the test data set showing 8 Regions-Of-Interest._ [](#toc) + +###Tracking Cell Drift### + +1. *[Download](http://sourceforge.net/projects/cellsampler/files/test_data2.zip)* the example dataset for this tutorial. Unzip the archive and place the images somewhere you can find them. ++ Create an directory to store output files created by the plugin. ++ Start ImageJ and from the ImageJ main menu, select _Plugins->Cell Sampler_. ++ Wait for the 2 images... </pre>Gareth SmithWed, 15 Aug 2012 14:09:30 -0000https://sourceforge.net81c9ab1ecaff746f174a3134e7c809fac2e4fdf5