Excel Data Window

The Excel Data Window can be used to collect plot, segmentation, object and cell counting data in a spreadsheet. The Excel Data Window is also useful to collect data for multiple runs of the same Pipeline on different stage positions of a multi-dimensional image set (see below at Formatted output).

1. To open Excel Data Window use the Tools/Excel Data Window main menu item. Microsoft Excel (Office 2003 to 365 have been tested) has to be installed on the system.
2. To save the spreadsheet use the File/Save Excel Data main menu item.
3. To erase contents of the spreadsheet select all cells by clicking the top left corner of the spreadsheet and press delete.

The following functions use the Excel Data Window to output results (instead of textual output) when Excel Data Window is opened:

• Measure Objects
• Count Colocalizing Objects
• Strip to Well Cell Count
• Plot
• Ratio Plot
• Correlation Plot
• Plot Segment Intensities
• Plot Morphological Parameters
• Simple and Advanced Segmentations
• Count Division and Cell Death
• Plot Tracking Parameters

Formatted Excel output:

Plot functions capable of plate formatted Excel output have following parameters, and setting them Yes will result formatted output:

• MD output: Organizes data in table according to Multi-Dimensional Open parameters. Channels appear next to each other. Analysis of different positions results data in rows below the previous analysis
• Plate output:  Organizes data in table according to multiwell plate layout. Each plot channel generates a new worksheet, where the plate is plotted for each time point. For this output it is essential to properly set up well names in the Plate tab of the Multi-Dimensional Open dialog.

Example output of  measurement of average velocity of cell migration using tracking. The top row indicates plot window caption and the used pipeline. The heatmap was added after printout. A single nd2 file recorded by Nikon Elements in 96wells was processed in unsupervised manner.