- This program has been imagined to make
easier the analysis of three channels microscopic fluorecence images.
It generates master panels called "Presentations" (_pl), from rgb
images, including 4 quadrants presenting the 3 singles channels (in
grey or pseudo color), and a rgb composite representation. These
"Presentations" are calibrated according to the objective used for
the acquisition of the images. All these informations, once set, are
encoded in the panels images. A second function allows to obtain the
the same kind of panels, from a region of interest called ROI (_zone)
selected on a "Presentation".
Quick Start:
A sample image is avaible for running the program on the ImageJ web site at: http://rsb.info.nih.gov/ij/macros/images/myotube.tif.zip
- To obtain a "Presentation" master pannel from a rvb image, press "p" on the keybord:
Left picture: three channels image window (12.5%, real size; 1110 x 790 pixels). Right picture: "Presentation" window (12,5%, real size; 4455 x 862), the red rectangle area (see an enlarged view below) presents a scale bar, the calibration scale in µm, the objective used for the image acquisition, the date of treatment [ref 3], and the microscope model used. Enlarged view of the red rectangle area on the "Presentation": ----------
- To obtain a ROI panel from a user selection made on a "Presentation" press (r) on the keyboard:
This figure shows a ROI selection (yellow rectangle on the top picture) obtained with the rectangle tool (grey in the tool bar). By pressing on "r" on the keybord, the panel shown in the lower picture of the figure is obtained.
- The tools provided allow to explore in a dynamic and simultaneous way the signal location of the 4 generated quandrants:
- Use the blue MultyCursor tool [ref 5] to colocate visually and dynamically some structure of interest.
- Use the green Arrow tool [ref 6] to draw at the same place in the 4 quadrant some customisable arrows.
- Use the magenta ArrowMaker tool to obtain a MultiCursor tool which draws customisable arrows when you unclick.
- Use the blue FreeHandArrow tool [ref 4] to draw a single arrow.
The use of the arrow
tool, examples:
- Use of the preview option :
This example of arrow parameters shows the result of a preview. These previews allow a user to build his own arrow collection.
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The orientation is based on the principle of the compass-card. The pixel pointed by the cursor has to be considered as a target. The choosen orientation, is the direction towards which the arrow points to it. This picture gives a summary of the 8 possible directions.
To obtain a filled arrowhead, choose an Arrowhead Filling Level greater than the Arrow length.
To obtain an arrow without tail (only arrowhead) set Tail Size (Length) and Tail Size (Width) to '0'.
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References:
[1] Wayne Rasband, 29 April 2005, ImageJ News: v1.34m, 29 April 2005: Added the Dialog.Box macro functions. The DialogDemo macro provides an example.
[2] Wayne Rasband, 10 June 2005: Improvements of these functions (remember of the last choices) were provided in this ImageJ update:ImageJ News: v1.34p, 10 June 2005.
[3] Bill Heeschen, 17 May 2005, ImageJ News: v1.34n 17 May 2005: The GetDateAndTime macro, contibuted by Bill Heeschen, demonstrates how to display the date and time.
[4] Wayne Rasband, 10 June 2005, ImageJ News: v1.34p, 10 June 2005: The ArrowTool draws arrows.
[5] Gilles Carpentier, 10 June 2005, ImageJ News: v1.34p, 10 June 2005: Gilles Carpentier contributed the MultiCursorTool macro, which displays multiple synchronized cursors.
[6] Gilles Carpentier, 10 June 2005, ImageJ News: v1.34p, 10 June 2005: Gilles Carpentier contributed the Arrow Maker Tool macro. Examples are at image.bio.methods.free.fr/Arrowsdoc.html.
[7] The RGB image sample, is a composite of three microscopic images of the same field in fluorescence mode. The example contains a triple lableling of a differentiated mouse myogenic cell line. Cell culture and immunochemistry; Juliette Peltzer, images from the courtesy of Dr Angelica Keller. For more details about the cell line, contact Dr Angelica Keller at keller@univ-paris12.fr.
This image, is avaible, for trying the program, on the ImageJ web site at http://rsb.info.nih.gov/ij/macros/images/myotube.tif.zip
Acknowlegments:
- I want to thank Wayne Rasband for his precious advices and continious improvements in the macro language of ImageJ, allowing to make very usefull complex projects.
- Special thanks to Alessandra Albano for the English correction of this page.
