In the scenario in the image below, we’ve selected 5 ROIs in measurement 7. ROI 2 responds to the stimulus with a fluorescence increase, and a decrease below baseline after the stimulus, ROI 3 has an OFF response (increased fluorescence after stimulus offset), “MyFirstROI” has slow response to the stimulus, and a slow decay. When your mouse clicked into the traces window, you can adjust the axes ranges. In the bottom left there is an “autoscale” button, useful if you’ve lost all of your traces.

The grey area is the stimulus. Stimulus timing information is taken from the list file (Synthetic_data_strip.lst.xls).

There is a vertical yellow line (arrow – at the beginning it is located at position 0). Click that line, keep clicked, and move it sideways to select the frame that is displayed in the frame panel. Use the color bar to the right of the “current frame” window to change color boundaries and color scale (right click on color palette). Play around with your data – many of the possibilities in this section are intuitive in the sense that they use common practice effects for right-mouse click, for scrolling, for selecting, etc.

BTW: at the bottom, you can see the frame number that is selected (arrow). This is useful, for example, to identify the frame number with the maximum response.

Saving ROIs

We would need to save the ROIs next, in order to work with them later. We illustrate this with another scenario, which is shown the image below.

Here the view in “current frame” is: all measurements overlayed (just select all measurements in the select data window, by using the shift button while clicking on measurements), each with its own color as indicated in the “select data” frame, traces shown for ROI 5, as indicated in the “ROI label” window, colors of the traces as for the frames from “select data”. The frame shown is indicated by the vertical line in the traces window (frame 34). The ROIs are shown in the frame view. (BTW: you can change ROI position and size any time using the mouse).

Use the pull-down menu “VIEW-Related” to save the ROIs. There is a choice if you have both circular and polygon ROIs, whether you want to save only the circular ROIs or all. This opens a window where you have to select which ROIs to save. (Advanced users may save separate ROIs for different measurements even within one animal; for the tutorial, choose: “save FOR ALL measurements of this animal”).

If you have a polygon ROI, you can save that one as an .area file. That is useful if the brain area is surrounded by non-brain, and the non-brain contains artefacts that should not be considered in some steps of the data analysis.

Where are ROIs saved? That is stated in the .yml file, in the flag STG_OdormaskPath. (After saving, a pop-up window also reports the saving location)

Previous page	Contents	Next page
Components of ILTIS window	Contents	Generating Overviews