Main Menu: View >
Use this window to analyze dot blots and other basic arrays
or whatever kind of images arranged in grids you have.
The Array Analyzer windows has a menu bar and, on the left,
four tabs: Array Settings,
Settings, View Settings
The first step is to load an image or selection into the
Analyzer window. Several buttons and Menus are going to stay disabled
until an image is loaded.
After loading an image you should
define the location of the array of dot blots (or whatever array of objects
you have) in the image, either automatically or by resizing and positioning
a grid enclosing the objects. By default the software will draw a grid
centered in the image. You should use the grid handles to position it
correctly over the image and set the number of columns and rows and the
diameter of the objects, in the Array Settings
To locate the objects automatically click
(under the Array Settings
tab) to open the Find Objects
Slide the controls on the Find
Objects window until the objects on the image are located as precisely
as possible. If you want to save the settings to use them with another
images you can use the Save As
and Load buttons to do that.
Objects works best with objects regularly arranged in grids, objects
haphazardly arranged may not be found correctly.
After closing the Find
Objects window you can adjust the position of the objects, if needed.
Continue reading to learn how to do that.
Adjusting the grid and objects
Depending on the tool selected in the Tool bar (on the left,
below the menu bar), you can manipulate in different ways the arrays of
objects. The tool bar has three toggle buttons, each one of them selects
a different tool, and also has a Calculate button:
The button on the left (shown selected in the above image)
corresponds to the array sizing tool. When this tool is select (it is
down), you can resize and move the array grid to adjust where the objects
are drawn. This is the tool that is selected by default after you load
The button in the middle is the Show/Hide button. By clicking
on any objects in the array it will be shown or hidden them (hidden objects
will be excluded from calculations).
The Selection button is the rightmost one. By clicking any
object it becomes selected, and if it was hidden it will be shown again.
Selecting on object is useful to get the data from it or to get its histogram.
The Calculate button
will perform calculations on the array ob objects, based on the settings
specified in the Calculation Settings
tab and will show the result in a separate window, from where the
data can be saved or printed. Learn
By default, the Draw Grid button is selected when
Analyzer window appears for the first time and a default size grid
is drawn on the image automatically.
That means that if you click and drag over the image a grid
selection box will be drawn. The following steps show how to draw and
setup a grid selection box:
After setting the placement of the array of objects, click
on Calculate button to calculate the statistical data and show
the result in a separate window.
can select what kind of statistical values are going to appear into the
spreadsheet in the Calculation Settings
Only the statistical measurements selected in this tab
will appear in the spreadsheet. The Decimal Positions text box
sets how many decimals will be shown. After selecting or deselecting items
click Calculate to open a new
window with the calculation results..
Each object will be assigned a percentage value, relative
to the Mean value of the darker object, which will have a 100%
value. If some objects are lighter than the background they may return
negative Dot% values, but only when Subtract Background is unchecked.
The same object will return zero Dot% values if Subtract Background is
checked, since any pixel inside an object that is lighter than the background
color will not be taken into account, only pixels darker than the background
color will be processed.
The Background color will affect how the Dot%
is calculated and if Subtract Background
is checked, the background pixel value will be subtracted from
all pixels in the objects. If Subtract
Background and Dot% are
unchecked the background color will not affect the calculation at all.
If all pixels in an object are lighter than the background,
the object will return no data (all values set to 0), when Subtract
Background is checked or return a Dot%
value less than 0 when Subtract Background
Background Subtraction will not work correctly unless the
image Background color is properly set. To do so click the Set Color
button in the Calculation Settings
tab, and draw a rectangle enclosing a representative area of the
Opens a Histogram window to show the selected object histogram.
Calculates the statistics value for only the selected object.
Allows inverting pixel values and modifying the pixels range. See Adjust pixel values window.
Sets which image channel will be used to perform the calculations.
Use other channels than Grayscale only if the image is a color one.
See also Color Channels
factor doesn't influence how Pixel Profile
or Array Analyzer work. It only affects values written into the Measurements Pane.