Grid Analysis Overview

When an image with a Grid Analysis is the current image, the Grid Analysis tab is shown on the ribbon. To apply a Grid Analysis to any image, click the quick launch button at the top of the window and select Grid from the drop-down list. Or, open the Analysis tab and select Grid from the drop-down list in the Type group. The last used parameters are used to create the new analysis.

Image Studio 5.0 Grid Analysis tab

Grid Group

A grid is placed on the image based on the last used settings when a Grid Analysis is applied.

  1. Click the Redraw Boundary button and click and drag a bounding box on the image to draw a new grid. Adjust the grid by selecting the bounding box and dragging the green arrows on each side. Move the entire grid by dragging the double arrows that appear when hovering on the image.
  2. Adjust the number of rows and columns by entering new values or using the up or down arrows to incrementally increase or decrease the number of rows or columns.

  3. Click on the Grid Template button to choose, save, or delete a template that determines the Grid, Spot, and Background method settings.

    Templates are useful for quickly selecting the settings that are commonly used, however, you do not need to use a template to set up a Grid Analysis.

  4. The Grid Template button resets to Custom when any of the Grid, Spot, or Background method settings are changed. To save the current settings to a new template, click the Grid Template button and choose Save Current Template... from the drop-down menu.

    5. Image Studio grid analysis save current templates

  5. Enter a name for the new template and click OK.

    6. Image Studio 5.0 Template Name dialog

  6. Click on the small arrow at the right edge of the Grid group to open the Advanced Array Definition dialog where you can set the spot size and the spacing between spots numerically.
  7. Image Studio 5.0 Advanced Grid Definition

Spot Group

Use the Circle or Square buttons in the Spot group to select the shape of the spots. Use the Larger or Smaller buttons to incrementally adjust the size of the spots for a better fit.

Auto-Adjust Group

Automatically moves the spots to the areas of high pixel intensity near them.

Grid Background Group

The following options are available in the Background group.

  • Image Studio Set Background IconBackground list - Choose a background subtraction method from the Background list.
    • Average - Uses space surrounding a spot as background.
    • Median - Uses space surrounding a spot as background.
    • User-Defined - A spot or spots must be designated as background.
    • None - Unless data are going to be exported for analysis using a third-party software, do not choose None.
  • Image Studio Assign Shape iconAssign - When the User-Defined background method is chosen, this button is used to assign a spot to be used for background calculation.
  • Image Studio Remove Background iconUnassign - Removes a User-Defined background spot from the background calculation.

Show Group

Use the controls in the Show group to specify what to display on the image. You can display Spots, Labels, Quantification, Grid Border, and Local Background (see Show Group for further details).