Downloads

Intestinal transit

You need ImageJ to use this software. Each archive contains a README with installation instructions.

To measure intestinal transit, follow the described protocol below.

Two full-field images - one in normal illumination mode and another in fluorescent mode - are taken and subsequently matched for analysis.

The fluorescent intensity throughout the entire GI tract can now be analyzed and calculated as follows:

Right-click the Line Selection Tool and select Segmented Lines.
Select the center line through the GI tract (fluorescent mode image).
To calculate the intensity profile, use the original ImageJ Plot Profile tool (Analyze->Plot Profile). Data are expressed as the percentage of fluorescence intensity per segment (stom, stomach; sb, small bowel segments 1-10; caec, caecum; col, colon segments 1-2) and plotted in a histogram.

Addendum

The following ImageJ macro can be used for calibration:

Calibrate Scale Tool

Select the Calibrate Scale Tool. Calibrate the screen width according to the used zoom factor (CCD camera). Enter the known distance in the dialog.

Contractility recordings (samples)

A MPEG4 viewer is needed to play these movies. Apple Quicktime is known to work.

Movie of intestinal contractile activity in control mice.
Movie of intestinal contractile activity in operated mice (ileus).

Contractility imaging and spatiotemporal mapping

Each archive contains a README with installation instructions.

AmplitudeProfiler:
This plugin can be used to quantify the contraction amplitude (%) of the small intestine.
The protocol is described below:

Import a video recording (File->Import->Using QuickTime) in ImageJ at 25 frames/s.
It is recommended to enable the option "convert to 8-bit grayscale".

Convert the loaded 8-bit grayscale images to (black-and-white) monochrome images (Image->Adjust->Threshold).
Adjust the lower and upper threshold value to become an optimal result.
Warning: artefacts overlapping the small intestinal border (black spots) or intestinal bleedings (white spots) will cause errors. Use the CalibrateScale Tool to calibrate distance (see above).

Select the area of interest (rectangular selection) and execute the AmplitudeProfiler plugin (Plugins->Compile And Run->AmplitudeProfiler.java).
A first window will show the mean diameter (pixels, mm) of the selected intestinal segment in the current frame.
A second window shows a graph with the contraction amplitude (%) for every pixel along the selected segment, calculated by the following formula:

diameter_max- diameter_min

diameter_max

Spatiotemporal Contractility Mapping Software (ContractilityMapping):
This plugin allows to see intestinal contractility in function of time (3-D).
The protocol is described below:

The plugin requires a stack of monochrome images. Follow the first two steps as described in AmplitudeProfiler.
Select the area of interest (rectangular selection) and execute the ContractilityMapping plugin (Plugins->Compile And Run->ContractilityMapping.java). A dialog window will pop up, allowing the modification of various parameters. It is possible to generate 2-D or 3-D plots, which can be saved in Postscript (PS) or Encapsulated Postscript (EPS) format.

For further technical information about the described software above, contact Bart Blanckaert.