gc icon Gilles Carpentier Research Web Site: Computer Image Analysis - Methods and Examples. ima

ijImage, Stack and Timelapse Arrow Labelling Tool for ImageJ §1 - Documentation:

Description:

This toolset allows to draw "histological" arrows on images, stacks and movies. The forms and others characteristics of arrows can be set through an interactive graphic interface, giving a dynamic preview:
palette

This sample image comes from the demo images available from the "File -> Open Samples" menu of ImageJ.
This confocal LSM timelapse sample comes courtesy of Tim Chico §.
(Wait until the movies are loaded and let them auto start. Stop by clicking, restart by double clicking, and move image by image with the left and right keyboard arrows.)

Notice:
   
    Menus description:
 
	- Movie and Stack Menu
The "Movie and Stack Menu" regroups the functions specific to movies and stack:

menu1

Note about opening movie function: this menu contains some options to record/open movies. Opening a movie with this toolset, required QuickTime 7 (at this link for Mac OSX, and this link for Windows) and QuickTime for Java.
Windows user have to install also the QuickTime plugin. QuickTime plugin is included with the Mac OS X version of ImageJ, version 1.34 and later.
It is adviced to update QuickTime 7 to 7.1.5 or higher.
- "Open a Movie as Stack" displays a dialog box to open a movie, using QuickTime resources, which will be opened as a stack of images.
- "Save a Stack as an ".avi" Movie" records a stack as an avi uncompressed movie into the same repertory than the original one, with an incremented suffix number.
- "Download/Open Demo Timelapse Movie" and "Download/Open Demo Timelapse Movie Arrowed" give respectively a training movie and an example of arrowed movie. Initial movie, obtained by LSM microscopy, was provided by Tim Chico (§).
- "Animation Speed Setting" sets the stack/movie animation speed using .
- "Animate the Stack" checks for the arrow effect on a stack, using activating the animation mode.

                - Arrow Drawing Menu
The "Arrow Drawing Menu" regroups the arrow drawing utilities:

menu2
  
- "Set Drawing Arrow(s) Location" is the first step to draw arrows: move, staying clicked, onto the image, until the cursor points the correct target of the arrow. Unclick, and adjust settings using the menu and the graphic interface which then will appear.
- "Draw Arrow(s) at the Current Location" draws a arrow at the current location when the user graphic interface has been canceled, or the cursor erased for any reason.
- "Restore the Last Cursor Location" restores a visual (non active) cursor at the last location.
- "New User Graphic Interface" is the default interface to set the arrow characteristics.
- "Standard User Interface" allows to use the dialog box interface of the "ArrowMakerTool"§2 instead of the graphical interface (see ArrowMakerTool documentation) .
- "Display Coordinates" gives the coordinates x, y  of the current location (same as displayed in the status bar).
- "Change the Color of a Arrow" allows to change the color of a draw arrow, by clicking on it.
- "Undo the Last Arrow" erases the last drawn arrow (only for single image or slice).

            - Cursor Color Menu
- The "Cursor Color Menu Menu" allows to manage the cursor color to make easier the visual location of the target area, depending of the background color of the image.

menu3
- "Restore Initial Selection Color" reset the color selection to the start-up ImageJ setting.
- "Get Curent Selection Color" gives the name of the currect color selection.

    Tool bar icons description:

                - Abort Process

menu4

- "Abort Process" ImageJ tool bar icon allows to cancel too long processes (downloads...).
                - On Line Documentation

menu5

- "On Line Documentation" ImageJ tool bar icon allows to open the present web page, from ImageJ, with the default browser of the user computer.

                - Version and Update Infos
menu6

- "Version and Update Infos" ImageJ tool bar icon looks for new versions of the "Image, Stack and Timelapse Arrow Labelling" toolset.

                - About "Image, Stack and Timelapse Arrow Labelling"
menu7

- "About Image, Stack and Timelapse Arrow Labelling" ImageJ tool bar icon gives a short notice and informations about the author and contributors.

Tutorial:

    The following part shows how to draw the permanant cyan arrow of the demo movie presented at the top of this page:
- 1) Download the demo movie from the "Download/Open Demo Timelapse Movie" submenu of the "Movie and Stack Menu", as shown into the following screen shots.
movie menu
- 2) Select the "Set Drawing Arrow(s) Location" from the "Arrow Drawing Menu".

ArrowDrawingMenu
-3) Move, staying clicked onto the stack, until the cursor points to the correct target of the arrow, that is indicated by the coordinates printed into the status bar (red arrow, x=32, y=171), see left picture below. Unclick,  and choose from slice 1 to 174 in the popup menus. Adjust the settings using the graphic interface which then will appear: arrow target to North, Tail Lenght to zero, and color to Cyan (green arrows onto the right picture below).

cyan----setcyan

- 4) Option: set the color cursor to obtain the best visual contrast (next picture).

coulorcursor

Example:

    Reproduce the arrowed demo movie:
   
The tables available at this link give the coordinates and settings of arrows used for the demo. Proceed as described above.
The movement effects are obtained using the "Change the Color of a Arrow" submenu from the "Arrow Drawing Menu".

First version: 24/04/2007

Code available on the ImageJ web site at the http://rsb.info.nih.gov/ij/macros/toolsets/Image, Stack and Timelapse Arrow Labelling.txt

References:

§1. 17 May 2005, ImageJ News: v1.34n, Wayne Rasband: The BigCursorTool macro simulates a full window cross-hair cursor using a polygon selection.
§2. 10 June 2005, ImageJ News: v1.34p, Gilles Carpentier contributed the Arrow Maker Tool macro. Examples are at image.bio.methods.free.fr/Arrowsdoc.html.
§3. 18 October 2005, ImageJ News: v1.35e, Gilles Carpentier contributed the Change Color Tool macro.
§4. 14 July 2006 ImageJ News: v1.37k, Gilles Carpentier contributed the URLtools macro set, which adds online resources to the ImageJ tool bar.
§5. 12 April 2007 ImageJ News: 1.38o, Gilles Carpentier contributed the SelectionColorMenuTool macro, which adds a toolbar menu for changing the selection color.

§ This toolset, based on the "ArrowMakerTool" was adapted to stacks and movie at the request of Tim Chico, PI in vascular biology, University of Sheffield, UK. Tim Chico also provided the downloadable movie example. More details about this sample are available at Tim's web link: http://www.cdbg.group.shef.ac.uk/research/chico/

ij §1 ImageJ (http://rsb.info.nih.gov/ij/) is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. The author, Wayne Rasband (wayne@codon.nih.gov), is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

ima Page author:
Gilles Carpentier, Faculte des Sciences et Technologies,
Universite Paris 12 Val-de-Marne, France.		 bioch
Microscopy Image Acquisition
and ImageJ contributions
 mail Computer Data Acquisition
for Biochemistry Practice Works

Special thanks to Alessandra Albano for the English correction of this page.
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