Creating Isochronal Map

Creating Isochronal Map

Authors: Côme PASQUALIN - François GANNIER (gannier at univ-tours dot fr) University of Tours (France)

See also: Others productions for ImageJ from the authors

Utilisation: Description / Installation / Utilisation of the plugin

Example

Isochronal Map with calibration.
Procedure

Requirements: File must be a stack and must be calibrated in each dimension (Use Ctrl+Shift+P) .
This analysis can be done on a squared selection.

Optional add-in requirements: To use the 3D filter (XYT) Savitzky-Golay, download "savitzky_golay.zip" from Matt Smith's HTML pages and extract files to the imageJ plugin folder. You will need also to install the Java Matrix (JAMA) package available here.

Before using tool: In "Analysis options" (button 6 of Spiky menu), configure "Min peak amplitude from baseline". Try first with a value between 10 and 20% (even lower if using smooth filter).
Use "Plot Result/Profile" tool to see the signal and find limits for one peak to fill the time zone range in the next dialog box. Active the Live mode (bottom of the plot window) and move the cursor to find image numbers.
Alternately, you can use "Auto Fill for IM" in the contextual menu to automatically fill this values.

Using tool: Choose "Isochronal map" and fill the setup dialog ("Mapping" window in the figure below).
"Sens of analysis" must be automatically detected, change if not.
Choose method, binning, Pre and Post processing.
Leave the sensitivity to the default values (5), this should be changed if detection isn't adequate.
Click "Ok".

After using tool: The calibration window can be obtained by the "create calibration bar" in the menu. Next steps are not necessary but allows to better see the transitions.
Use "Brightness and Contrast " dialog box (Ctrl+Shift+C) to find min values corresponding to the starting point (black pixels when you move "Minimum" cursor) then place the cursor on the lower value of the isochronal map and use "Starting point" in the contextual menu.
Always using "Brightness and Contrast" move 'Maximum' cursor to find the max then use "Greylevel filter" with same values to exclude extra values.
According to options, an overlay can be paste to the source image.

Options

- suffix: custom suffix added to the name

- Sens = peak is up (positive) or down (negative)
- Method = choose one method of detection

- Axial binning (x±value) = xy binning

- Temporal binning (x±value) = z binning

- Sensitivity = define the sensibility of detection

- Post-processing: a smooth filter is applied after analysis
- Interpolate: an interpolation is applied after analysis
- Paste overlay: map is paste on source image as an overlay

- Analysis time zone: range for the analysis

- Recurrence: repeat analysis on shifted range

- Set color to frame: each color corresponds to the image number

Testing: To test making isochronal map, a stack of images from an entire mouse heart is provided. This video was recorded at 1 kHz, heart is perfused with a calcium dye.

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Authors:	Côme PASQUALIN - François GANNIER (gannier at univ-tours dot fr) University of Tours (France)
See also:	Others productions for ImageJ from the authors
Utilisation:	Description / Installation / Utilisation of the plugin

Requirements:	File must be a stack and must be calibrated in each dimension (Use Ctrl+Shift+P) . This analysis can be done on a squared selection.
Optional add-in requirements:	To use the 3D filter (XYT) Savitzky-Golay, download "savitzky_golay.zip" from Matt Smith's HTML pages and extract files to the imageJ plugin folder. You will need also to install the Java Matrix (JAMA) package available here.
Before using tool:	In "Analysis options" (button 6 of Spiky menu), configure "Min peak amplitude from baseline". Try first with a value between 10 and 20% (even lower if using smooth filter). Use "Plot Result/Profile" tool to see the signal and find limits for one peak to fill the time zone range in the next dialog box. Active the Live mode (bottom of the plot window) and move the cursor to find image numbers. Alternately, you can use "Auto Fill for IM" in the contextual menu to automatically fill this values.
Using tool:	Choose "Isochronal map" and fill the setup dialog ("Mapping" window in the figure below). "Sens of analysis" must be automatically detected, change if not. Choose method, binning, Pre and Post processing. Leave the sensitivity to the default values (5), this should be changed if detection isn't adequate. Click "Ok".
After using tool:	The calibration window can be obtained by the "create calibration bar" in the menu. Next steps are not necessary but allows to better see the transitions. Use "Brightness and Contrast " dialog box (Ctrl+Shift+C) to find min values corresponding to the starting point (black pixels when you move "Minimum" cursor) then place the cursor on the lower value of the isochronal map and use "Starting point" in the contextual menu. Always using "Brightness and Contrast" move 'Maximum' cursor to find the max then use "Greylevel filter" with same values to exclude extra values. According to options, an overlay can be paste to the source image.