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






--------ij--Dot Blot Analyzer for ImageJ - Documentation:--------ijconf
 


Description:

! This tool is no more maintained. It has been updated with the name "Protein Array Analyzer" at this link.

This tool allows a fast and easy dot blot analysis from various sizes, through an interactive graphic interface, giving a dynamic preview of measurement results:





bl28


Analysis of the demo image from the ImageJ sample collection.

The simple method of analysis, performed by integrating the grey levels of pixels (volume) surrounded by a circular selection, has been described onto the ImageJ website [1].



Notice:

    Dot Blot Analyzer menu tools:

- The "Dot Blot Analysis Menu" regroups analyse and training functions:

me1

- "Analyse a Dot Blot": Displays the graphical interface required to analyse an opened dot blot image.

- "Download/Open The ImageJ Demo Dot Blot Image (28 wells)": Opens the ImageJ Dot Blot image sample (28 dots) [2].

- "Download/Open Demo Dot Blot Image (96 wells)"): Opens a demo image (96 wells) useful to test the program with other settings than the defaults ones [].

- The "Measurement Documents Menu" regroups tabs and analysed images management functions [3]:

me2

- "Save Results Documents": Saves every document concerning one analysis (model, tabs, images) into a folder at the user choiced master repertory.

- "Save Results Documents at the Dot Blot Image Location": Saves every documents concerning one analysis (model, tabs, images) into a folder placed at the dot blot image repertory.

- "Close Results Documents": Closes every document concerning one analysis (models, tabs, images).

- "Save Grid Results Table as Excel Type File": Saves the current grid analysis table at the user's choice location.

- "Save Single Measurements Table as Excel Type File": Saves the current manual analysis table at the user's choice location.

- "Save Grid Results Table as Excel Type File at the Dot Blot Image Location": Saves the current grid analysis table in the dot blot image repertory.

- "Save Single Measurements Table as Excel Type File at the Dot Blot Image Location": Saves the current manual analysis table.

    Tool bar icons description:

- "Abort Process": cancel demo downloading or erease the palette's cursor.

me3

- "On Line Documentation": on line documentation and tutorial [2].

me4

- "Version and Update Infos": look for new beta versions.

me5

- "About "Dot Blot Analyzer"": out of line short documentation.

me6


    Graphical Interface:

Once activated, the "Dot Blot Analysis Menu" builds a graphical interface "Palette"containing a dot blot preview [4]. Here are the "clickable" available actions:

- Volume measurement using the composite cursor [1][5]: Activate the measurement cursor by staying clicked and moving into the dot blot preview area. Cursor ploted and real coordinates are dynamically showed into the display area (left below), the measured volume, is available when unclicked (right below).

curs1----------------curs2
------

- Customize the composite cursor aspect:

- Optimize the visual aspect by choosing appropriate colors for the circle and the the cross hair of the cursor componants,  using the colored rectangles.

corscol

- Find a pertinant circle radius by clicking onto the circle containing radius icone. ---------
- Adjust the cursor circle size using the "+" and "-” sub-buttons.
cursize

- Optimize the dot blot preview visualization:

- Normalize the histogram from the "stretch curve" icon.
- Adjust the saturation level using the "+" and "-” sub-buttons.
cont
- Choose the appropriate Look Up Table (LUT) by clicking into the LUT ramps icone.-- lut
- Restore the initial preview properties with the counterclockwise symbol.rest

- Single measurement recoding in a tab:

sing1

- Click "Add" to generate a tab with the current value given by the cursor, "Remove" to delete it
(CTRL click
undo the delete action).
- Erase all the measurements of the tab by the red "X". This action in undo by "CTRL click".
---
sing2

- Grid measurements mode:

grid1


- Adjust the column ("nCol.") and the line ("nLin.") numbers, corresponding to the total or sub-area
dot
blot to analyse.
grid2
- Set the three required dots forming angle (hight-left, hight-right and low-left) using the three
green cross
hair icones.
grid3
- Marks can be adjusted, by re-selecting the appropriate cross hair symbol (Green cross hair: mark
to set. Red cross hair: set mark. Orange cross hair: mark in setting).
grid4
- Get a modelled image of the grid analysis by clicking on "Model".grid5

- "Shift" between the grid measurements mode and the single measurements mode can be performed
by clicking
onto "Measurements:" and "Grid:".
shift1---shift2
- "Cancel" box closes every thing concerning one analysis, including the Palette.cancel
- "Erase" box removes every drawn dot contours. They can be redrawn by clicking onto "Measurements:"
or "Grid:".
erase
- "End: Quit": finish an analysis (Deactivate the Palette, keeping an image or the current drawings). end



First version: 05/09/2008     tudor-ts

Code available on the ImageJ web site at the http://rsb.info.nih.gov/ij/macros/toolsets/Dot Blot Analyzer.txt




References:

1. Rasband W. Dot Blot Analysis, ImageJ documentation, Tutorial and Examples, available at the  "http://rsb.info.nih.gov/ij/docs/examples/dot-blot/index.html"
2Carpentier G. Contribution: the URLtools macro set, which adds online resources to the ImageJ tool bar. ImageJ News, July 2006 .
3. Carpentier G. Contribution: CustomTabStatFromResults, a macro set that demonstrates how to create, modify, open and save custom results tables. ImageJ News, November 2007. 
4. Carpentier G. Contribution: the Image, Stack and Timelapse Arrow Labelling toolset (online documentation), which allows the user to draw arrows on images and stacks. ImageJ News, May 2007.
5. Rasband W. Contribution: the BigCursorTool macro simulates a full window cross-hair cursor using a polygon selection. ImageJ News, May 2005.
. Sample dot blot with a 96 wells grid from courtasy of Mohand Ouidir.



ij
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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