Analyze_Calcium_Signals_In_Spines

Analyze calcium signals in dendritic spines. The images consist of time-series of calcium signals. Each image contains a selection that marks the point of stimulation. The tool finds the region to analyze close to the point of stimulation. It measures the intensity of the calcium signal in the whole region of interest and in the segmented spots.

The source code in git-hub can be found here.

Getting started

To install the tool save the file analyze_calcium_signals_in_dendritic_spines.ijm into the folder macros/toolsets of your FIJI installation and restart FIJI.

Select the "analyze_calcium_signals_in_dendritic_spines" toolset from the >> button of the ImageJ launcher.

• The first button (the one with the image) opens this help page
• The f-button finds the region to analyze near the stimulation point on the current image. The first roi in the roi-manager must be the one marking the stimulation point.
• The a-button runs the whole analysis of the calcium signal on the current image.
• The b-button runs the analysis of the calcium signal in batch-mode on a set of images in a folder.
• The r-button runs the region detection in batch-mode on a set of images in a folder.

Options

• width of region - The width of the region in which the signal will be measured.
• height of region - The height of the region in which the signal will be measured.

• first timepoint - The timepoint (frame) of the stimulation. All measurements are divided by the mean intensity of the signal in the frame before the first timepoint.

• channel - The channel of the image that contains the calcium signal.

• sigma Gaussian blur - The sigma of the Gaussian blur filter, used to detect the spots in the region of interest.

• thresholding method - The auto-thresholding method used to segment the calcium spots.

• min. spot size - Spots with a smaller area are removed from the analysis.

• measure whole region - Measure the mean intensity in the whole region of interest.

• measure spots - Measure the mean intensity in the segmented spots.

• display plots - Display the plots of the measurements over time.

• file extension - The file extension of the input images. Besides the configured image type, tif-images with the extension .tif are also allowed.

Results

A results table with the measurements is written into the input folder. The first column contains the time starting at 0. The other columns contain the mean intensity in the region and in the spots for each image.

An image indicating the measured zones is written into the subfolder control-images of the input folder. When running the batch find regions tool, the result images containing the detected ROIs are written into the subfolder regions of the input folder.