5.6. Dialogs

5.6. Dialogs
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This dialog allows to export signal measurements that are continuous in time and recorded in specific channels of the images, including in the backstroke.

See File+Export → Export Time Traces....

Figure 5.3. Analysus Mode, Export Time Traces Dialog

The export generates two files, a CSV file with the data and a text file with the channel name, unit and conversion information.

Using Physical Units, the first couple of exported lines of a CSV file may look like:

Camera-TimeTrace-20170405T140925-F000-F000-C2-C3-C4-C5.csv:

time [ms];ch2;ch3;ch4;ch5;
0;32.959;-5.99777;9.99141;39.2743;
0.1;50.6592;-1.69168;14.2185;47.8993;
0.2;49.4385;-1.69168;14.2954;47.7453;
0.3;52.7954;-1.69168;14.2185;47.7453;
...

The time in the first column denotes relative time in ms with respect to the first exported 'pixel'.

The accompanying text file Camera-TimeTrace-20170405T140925-F000-F000-C2-C3-C4-C5.csv.txt contains the following:

Channel;Description;Scale [ADCBit/Unit];Unit
2;"Tunnelling Current";0.305176;"[pA]"
3;"U_Sample";0.0768945;"[mV]"
4;"I_EC";0.076857;"[mV]"
5;"U_Tip";0.154017;"[mV]"

Note that the default filename encodes the time point of the first exported frame (20170405T140925), the range of frames exported (F000-F000) and the channels (C2-C3-C4-C5).

5.6.2. Analysis Dialogs

5.6.2.1. Area
5.6.2.2. Cluster Counter

5.6.2.1. Area

Figure 5.4. Analysis Mode, Area Dialog

5.6.2.2. Cluster Counter

Figure 5.5. Analysis Mode, Cluster Counter Dialog

5.6.3. Image Filters

5.6.3.1. Clip, Clad, Shift Filters

5.6.3.1.1. Clad Filter
5.6.3.1.2. Shift Filter

5.6.3.2. Scale Filters

5.6.3.2.1. Compand (Line) Filter
5.6.3.2.2. Sigmoid Filter

5.6.3.3. Threshold Filters

5.6.3.3.1. Binary Threshold Filter
5.6.3.3.2. General Threshold Filter

5.6.3.4. Smooth, Sharpen Filters

5.6.3.4.1. Mean Filter
5.6.3.4.2. Median Filter
5.6.3.4.3. Minimum Filter
5.6.3.4.4. Maximum Filter
5.6.3.4.5. Kuwahara Filter
5.6.3.4.6. Custom Filter
5.6.3.4.7. Linear Regression Image Filter

5.6.3.5. Morphology Filters

5.6.3.5.1. Dilation Filter
5.6.3.5.2. Erosion Filter

5.6.3.6. Derivative Filters

5.6.3.6.1. Derivative (Line) Filter
5.6.3.6.2. Derivative (Plane) Filter

5.6.3.7. Background Subtraction Filters

5.6.3.7.1. Linear Regression (Line) Background Subtraction Filter
5.6.3.7.2. Linear Regression (Plane) Background Subtraction Filter
5.6.3.7.3. Most Common Normal Background Subtraction Filter

5.6.3.8. Double Buffer Filters

5.6.3.8.1. Math Filter
5.6.3.8.2. DZ-Correction Filter
5.6.3.8.3. Fast Normalized Cross-Correlation Filter
5.6.3.8.4. Cross-Correlation (Spatial Domain) Filter

5.6.3.9. Frequency Domain Filters

5.6.3.9.1. Fourier Transform Filter
5.6.3.9.2. Inverse Fourier Transform Filter
5.6.3.9.3. Swap Quadrants Filter
5.6.3.9.4. Low-Pas Filter
5.6.3.9.5. High-Pass Filter
5.6.3.9.6. Auto-Correlation Filter
5.6.3.9.7. Cross-Correlation Filter

5.6.3.10. More Filters

5.6.3.10.1. Null Filter
5.6.3.10.2. Test Pattern Generator
5.6.3.10.3. Linear Regression + Diff (Line) Filter
5.6.3.10.4. Linear Regression + Diff (Plane) Filter

[ToDo: To be written ]

5.6.3.1. Clip, Clad, Shift Filters

Filter → Clip, Clad, Shift

5.6.3.1.1. Clad Filter

Figure 5.6. Analysis Mode, Filters: Clad Filter Dialog

5.6.3.1.2. Shift Filter

Figure 5.7. Analysis Mode, Filters: Shift Filter Dialog

5.6.3.2. Scale Filters

Filter → Scale

5.6.3.2.1. Compand (Line) Filter

Figure 5.8. Analysis Mode, Filters: Compand Line Filter Dialog

Line-by-line compression filter.

Background subtraction:

None
Mean
Median
Linear regression

Compression:

None
Maximum
Sigmoid: y = ymin + ( ymax - ymin ) / ( 1 + e^ -( (x - center) / strength ) )

5.6.3.2.2. Sigmoid Filter

Figure 5.9. Analysis Mode, Filters: Sigmoid Filter Dialog

Sigmoid (plane) compression filter.

Sigmoid: y = ymin + ( ymax - ymin ) / ( 1 + e^ -( (x - center) / strength ) )

5.6.3.3. Threshold Filters

Filter → Threshold

5.6.3.3.1. Binary Threshold Filter

Figure 5.10. Analysis Mode, Filters: Binary Threshold Filter Dialog

5.6.3.3.2. General Threshold Filter

Figure 5.11. Analysis Mode, Filters: General Threshold Filter Dialog

5.6.3.4. Smooth, Sharpen Filters

Filter → Smooth, Sharpen

5.6.3.4.1. Mean Filter

Figure 5.12. Analysis Mode, Filters: Mean Filter Dialog

5.6.3.4.2. Median Filter

Figure 5.13. Analysis Mode, Filters: Median Filter Dialog

5.6.3.4.3. Minimum Filter

Figure 5.14. Analysis Mode, Filters: Minimum Filter Dialog

5.6.3.4.4. Maximum Filter

Figure 5.15. Analysis Mode, Filters: Maximum Filter Dialog

5.6.3.4.5. Kuwahara Filter

Filter+Smooth, Sharpen → Kuwahara

See [Young et al.], p.59 For an explanation of the Kuwahara filter.

5.6.3.4.6. Custom Filter

Figure 5.16. Analysis Mode, Filters: Custom Filter Dialog

5.6.3.4.7. Linear Regression Image Filter

Figure 5.17. Analysis Mode, Filters: Linear Regression Filter Dialog

Here is an example of the effects of selecting -sqrt(AA+BB) as output from the linear regression filter with a 3x3 pixel filter area.

Figure 5.18. Analysis Mode, Filters: Linear Regression Filter example showing -sqrt(AA+BB)

Here is an example of the effects of selecting +sqrt(AA+BB) and C as output from the linear regression filter with a 3x3 pixel filter area.

Figure 5.19. Analysis Mode, Filters: Linear Regression Filter example showing +sqrt(AA+BB), C

5.6.3.5. Morphology Filters

Filter → Morphology

5.6.3.5.1. Dilation Filter

Filter+Morphology → Dilation

5.6.3.5.2. Erosion Filter

Filter+Morphology → Erosion

5.6.3.6. Derivative Filters

Filter → Derivative

5.6.3.6.1. Derivative (Line) Filter

Figure 5.20. Analysis Mode, Filters: Derivative (Line by Line) Filter Dialog

5.6.3.6.2. Derivative (Plane) Filter

Figure 5.21. Analysis Mode, Filters: Derivative (Plane) Filter Dialog

5.6.3.7. Background Subtraction Filters

Filter → Background

5.6.3.7.1. Linear Regression (Line) Background Subtraction Filter

Filter+Background → Linear Regression (Line)

5.6.3.7.2. Linear Regression (Plane) Background Subtraction Filter

Figure 5.22. Analysis Mode, Filters: Linear Regression (Plane) Filter Dialog

5.6.3.7.3. Most Common Normal Background Subtraction Filter

Figure 5.23. Analysis Mode, Filters: Linear Regression Filter Dialog

5.6.3.8. Double Buffer Filters

Filter → Double Buffer

5.6.3.8.1. Math Filter

Figure 5.24. Analysis Mode, Filters: Math Filter Dialog

$Analysis Mode, Filters: Math Filter Dialog$

5.6.3.8.2. DZ-Correction Filter

Figure 5.25. Analysis Mode, Filters: DZ-Correction Filter Dialog

5.6.3.8.3. Fast Normalized Cross-Correlation Filter

Figure 5.26. Analysis Mode, Filters: Normalized Cross-Correlation Filter Dialog

5.6.3.8.4. Cross-Correlation (Spatial Domain) Filter

Figure 5.27. Analysis Mode, Filters: Cross-Correlation (Spatial Domain) Filter Dialog

5.6.3.9. Frequency Domain Filters

Filter → Frequency Domain

5.6.3.9.1. Fourier Transform Filter

Filter+Frequency Domain → Fourier Transform

5.6.3.9.2. Inverse Fourier Transform Filter

Filter+Frequency Domain → Inverse Fourier Transform

5.6.3.9.3. Swap Quadrants Filter

Filter+Frequency Domain → Swap Quadrants

5.6.3.9.4. Low-Pas Filter

Figure 5.28. Analysis Mode, Filters: Low-Pas Filter (Frequency Domain) Filter Dialog

5.6.3.9.5. High-Pass Filter

Figure 5.29. Analysis Mode, Filters: High-Pas Filter (Frequency Domain) Filter Dialog

5.6.3.9.6. Auto-Correlation Filter

Filter+Frequency Domain → Auto-Correlation

5.6.3.9.7. Cross-Correlation Filter

Figure 5.30. Analysis Mode, Filters: Cross-Correlation (Frequency Domain) Filter Dialog

5.6.3.10. More Filters

Filter → More

5.6.3.10.1. Null Filter

Figure 5.31. Analysis Mode, Filters: No-Operation Filter Dialog

5.6.3.10.2. Test Pattern Generator

Figure 5.32. Analysis Mode, Filters: Test Pattern Generator Dialog

5.6.3.10.3. Linear Regression + Diff (Line) Filter

Filter+More Filters → Linear Regression + Diff (Line)

5.6.3.10.4. Linear Regression + Diff (Plane) Filter

Filter+More Filters → Linear Regression + Diff (Plane)

5.6.4. Settings

Figure 5.33. Analysis Mode, Settings: Software

Figure 5.34. Analysis Mode, Settings: Calibration & Units

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