Analysis: Tools

The Tools module allows applying different advanced tools to analyze your data:

1. Trace: show a time series of parameters for spots found in a circular area selected from the localization data (not applicable to the raw images). To draw a circular area of interest on the localization data:
   
1. Toggle to render the localization data of interest.
   
2. Click on Trace.
   
3. Left-click on the rendering and drag the cursor to change the radius of the ROI selection.
   
4. Release the left button to confirm the selection. You may left-click on the rendering to move the selected ROI to a new position (from center to center). You may also left-click on the rendering and drag the cursor to re-draw a new circular ROI.
   
5. Press Enter to plot the following information in a pop-up window:
   
   
1. X/Y Position: a time series of X/Y positions read from the ROI (relative to the center of the ROI).
   
2. Photon Counts: a time series of photon counts read from the ROI.
   
3. Sigma X/Y: a time series of standard deviations calculated from the ROI.
   
4. Temperature: a time series of temperatures monitored from the ROI.
   
5. Acceleration Detected: a time series of motions detected from the ROI (should always be "0").
   
2. Line Histogram: show a histogram of intensities for spots found in a rectangular area selected from the localization data (not applicable to the raw images). To draw a rectangular area of interest on the localization data: 
   
1. Toggle to render the localization data of interest.
   
2. Click on Line Histogram.
   
3. Left-click on the rendering and drag the cursor to change the size of the ROI selection.
   
4. Release the left button to confirm the ROI selection. You may left-click on the ROI (near the dashed line) and drag it to move to a new position or left-click on the ROI (near the four dots) and drag it to change the size. You may also left-click on the rendering and drag the cursor to re-draw a new rectangular ROI.
   
5. Press Enter to plot the intensity histogram in a pop-up window: Distance along the axis perpendicular to the dashed line is binned, and localizations are summed along the axis parallel to the dashed line and plotted as frequencies (Freq.) at each binned unit of distances. You may change the size, position, and bins for the histogram on the top of the rendering.
   
   

   
   
3. XYZ Plane View: show the position of each localization along the XY, XZ, and YZ planes, similar to Line Histogram:
   

   
   
4. Tracking: for more detailed instructions, check here.
   
5. FRET Traces: for more detailed instructions, check here.
   
6. Calculate Drift Correction: for more detailed instructions, check here.
   

If at any point you are having issues with the calibration process, please do not hesitate to contact the CX team.

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