Matrix view
- Load the file calcium imaging.
This is a 28-trace optical recording of calcium fluorescence, and with this many traces it is hard to see what is going on in the standard chart view. - Select the View: Matrix view: Configure menu command.
This sets up the dimensions of the Matrix view (also available through the Window menu). - Set the matrix dimensions to 5 rows and 6 columns.
The default layout is a square matrix large enough to hold all the traces, , but since there are 28 traces, a 5 row and 6 column configuration is sufficient to show all the data.
If you wanted you could order the traces in vertical columns rather than by rows, and you could leave some empty cells at the start. Both these changes could be made within the matrix view itself, but it is easier to get the initial layout approximately as desired through the Configuration dialog. However, leave these at their default values for now. - Press OK.
The matrix view now displays. If you immediately Close the matrix view, and then select View: Matrix view: Show to re-display the view without configuring it first, the view retains the settings of the previous configuration. However, if you want this configuration to persist after closing the file, you must save the file itself after matrix view configuration. If you edit the cell display within the Matrix view, then you must click Store within the view to retain the edited settings.
- With the matrix view open, drag on a corner of the window to increase its size. You can now see all 28 traces, each displayed in its individual cell. The last 2 cells are empty, because there are 30 cells and only 28 traces.
It is apparent that some traces are mainly noise (e.g. traces 2, 3, 4 etc.) while some traces contain an obvious signal (e.g. traces 20, 21, 22 etc.). This was by no means clear in the standard chart view.
- Click Hide all -1.
The Show box in each matrix cell except that of trace 1 becomes unchecked, and in the main view all the traces are hidden except for trace 1. - Check the Show boxes in cells 20, 21, 22 and 26, then uncheck the box for cell 1.
The main view now shows traces which contain a clear signal.
- Uncheck the Layout mode box.
You can now see more of the data.