BZScan User Manual

Below is a step by step procedure for quantifying DNA arrays with BZScan. Many problems are solved by 1) changing to the correct tab in the left-hand section of the window, which you can pull-out, 2) using an option in the right-click menu.

1: Create a grid (.grd file)

Select the Grid tab, start a new grid, choose the number of levels (0-2) and build the grid level by level. Save the grid (right-click on tab).

2: Load the image (.tif or .inf file)

Select the Image tab, browse your file system and double-click on an image file. Images must be in 16-bit greyscale format.

3: Align the grid

Select the Alignment tab, browse your file system and double-click on a grid file (.grd). Automatic procedure: click on auto align. Manual procedure: move and resize the grid by hand. Use the right click options for a faster alignement When it is finished, click on go to fine-tune the alignement. You can save the aligned grid (.gra file) for future use.

4: Quantify

Select the region of the grid you want to quantify, then select the Quantification tab, click on Quantify, and save the results (right-click on tab). There is a (very technical) description of the outputs here.

5: Batch mode

Select the Batch tab, launch a batch window and input 1) A set of images (.tif, .inf, etc.), 2) A grid (.grd). You can repeat these operations several times, and save this information as a batch file (.bzb). Press go, and collect the results (one .qtf file for each image file, to be found in the same directory and under the same name as the image itself).

6: Analysis

Select the Analyze tab and choose two ("Plot") or more ("Plots") quantification files (.qtf) to display scatterplots of the results.