Array Analyzer

Menu: Image -> Array Analyzer.

Array Analyzer can analyze dot blots and other basic arrays or whatever kind of images arranged in grids you may have.

If one image is already loaded in the main window, Array Analyzer will offer to load it when you open its window. Also is possible to load images from the Array Analyzer window. When new images are loaded the previous array settings will remain, that allows to analyze many different images using the same settings.

After the array boundaries and all Array and Calculation settings are properly set, such setting can be saved to disk, in case they may be reused to analyze other similar arrays in different images. Use the commands File -> Save Settings As and File -> Load Settings to save and retrieve the settings.

Depending on the tool selected in the Tool bar (on the top left, below the menu bar), you can manipulate in different ways the arrays of items. The tool bar has five toggle buttons, each one of them selects a different tool.

Array Settings

After an image is loaded, use either the round (which is selected by default) or rectangular array drawing tools to mark the array boundaries over the image

After the array grid is drawn over the imager the selection tool will be automatically selected. Use the grid handlers (visible in its corners) to resize the grid. To move it use the round handlers that are drawn in the center of each item. The Array Settings (# row/columns, spacing, color, etc.) can be adjusted by using the controls in the Array Settings tab.

The button (shown selected in the image on the left) corresponds to the array selection tool. When this tool is selected, you can resize or move the array grid to adjust where the objects are drawn.

The two following buttons, and select a whole row or column of objects. Selected rows or columns can be moved and deleted.

The rightmost buttons and select if the array is going to be elliptical or rectangular. is the tool that is selected by default after you load an image.

After an array is drawn, the button will be automatically selected, to allow you to adjust the array position and size. The number of row and columns as well as the space between them can be set using the controls that are placed in the Array Settings tab (on the left).

To select a single array object, press SHIF while you click on it. The object can be resized, moved, or deleted.

Calculation Settings

After the array grid is correctly adjusted, click on Calculate button to calculate the statistical data and show an spreadsheet in a separate window.

To set what kind of statistical values are going to appear into the spreadsheet use the Calculation Settings tab (shown on the right).

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..

Dot%

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 checkbox is unselected. 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.

Background color

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 is unchecked.

Background Subtraction will not work correctly unless the image Background color is properly set. To do so click the button in the Calculation Settings tab, and then click on the area of the image that has the background color (a 3x3 pixel sample will be used to set the background color).

Color Channels

The color channel selected in the Channels menu will be used to perform the calculations. By default the Grayscale channel is selected.

Lane Profile

Lane Profile generates a graphic showing the average pixel intensity value along each array item in a column or row (from 0 to 255). This value is the exact inversion of the image pixel values, so higher values mean darker pixels. Lane Profile always uses the grayscale or RGB values, detecting automatically if an image is grayscale. The selected color channel it not taken into account.

The menu command View -> Lane Profile opens the window shown on the left, where is possible to select which column or row will be used to generate the graphic. Also there is possible to show a graphic with all columns or rows in the image.

Orientation only can be set if All Columns or All Rows options are selected. In such case several graphics will generated (one for each column or row). The graphics will be shown in a row, a column or a table, depending on the orientation option that is chosen.

Notes

Every time you resize the array, it will be reset to its default number of rows and columns. Any item that was deleted or resized manually, will go back to its default settings.
The conversion factor doesn't influence how Array Analyzer works.