XTensions for Matlab

(MathWorks)

The following XTensions are developed with Matlab® 7.0.1, and they require Imaris 4.1.3 or higher. Right-Click the links below and select "Save Target As..." (Internet Explorer) to download and save the files.

Stitcher XTension

BpStitchDataSets.m SticherXTensionHelp

This XTension lets users stitch together datasets acquired as separate tiles.

DataSet Functions

	BP3Dto2DProjection.m	Resize the dataset to 2 dimensions. 2 dialog boxes ask the projection plane XY, XZ or YZ) and the projection mode (MIP or Mean) if their values are not specified as input parameters.
	BPAttenuationCorrection.m	The layers to the top of the data set (close to objective lens) show often much higher intensities than layers deep into the tissue. This XTension can correct this attenuation effect. The correction is performed along the Z-axis.
	BPAutoCrop.m	This XTension computes the bounding box of voxels with intensity higher than the specified threshold, and cuts away the "useless" voxels at the borders. This helps to minimize the size of the dataset without loosing significant data.
	BPHistogramEqualizeLayers.m	Equalizes the histogram of voxel intensity layer by layer.
	BPNormalizeLayers.m	Normalizes the voxel intensities layer by layer (same mean and StdDev).
	BPNormalizeTimePoints.m	Normalizes the voxel intensities for each time point of a 4D dataset (same mean and StdDev).
	BPRGB2Gray.m	Add a gray channel to the dataset. Its intensity is given by a weighted sum of the intensity of the other channels. The coefficients of the sum are given by the user.
	BPSmoothTime.m	Smooth the intensity of each voxel along the time dimension using a gaussian filter.
	BPTimeProjection.m	Project all channels of a time dataset to a single time point. For each voxel the intensity is computed using a MIP or mean projection of all time points. The projection mode is asked to the user.
	BPTimeSubtractAverage.m	For each voxel, subtract the temporal average intensity. This function is used to eliminate motionless objects. For 2D time series try to use 'Image processing - Swap Time and Z' before and after starting the XTension to speed up processing.

Spots Functions

	BPSpotsCloseToFilament.m	The user has to create a Spots and a Filament component. This XTension segments the spots into two groups: Spots that are close to the filamentous structure will be colored red, the others blue. This might help to count spines.
	BPSpotsMerge.m	Merge all the spots objects that are in the same folder in a single spots object.
	BPSpotsOnEndsOfLines.m	Segment the dataset and subdivide the spots in groups of spots that lie inside (or around) the same line. For each spots group discard all but the two most distant spots, leaving more or less those on the line ends. The image is read from channel 1 and the segmentation is returned in channel 2; All other channels are removed.
	BPSpotsSplit.m	Split one spots object in sub groups of disconnected spots. Two spots groups are disconnected if the minimal distance between their elements is greater than the user-defined threshold.
	BPSpotsSplitIntoSurfaceObjects.m	For each surface object in the same folder of the spots, create a new spots object containing the spots that lies inside the surface. Works on surface objects: To obtain them, Split Isosurface or Create Surface Object from Contour Surface.
	BPSpotsCloseToSurface.m	Find the spots that are closer to a surface than a threshold, and create two new spots objects: One collects the spots close to the surface, the other the farer. If multiple spots or surfaces are selected, each pair [spots, surface] is analyzed: The number of spots objects created is 2 times 'number of spots' times 'number of surfaces'.

Filament Functions

	BPFilamentAnglesStatistics.m	Plot two histograms that display the statistic of the angles of a filament. The angles are divided in two types: Angles between the segments and angles between the branches.
	BPFilamentSpinesStatistics.m	Plot three histograms that display the distribution of the length, the average width and the volume (log scale) of the spines of a filament object. In addition, a plot shows the distribution of the average width to respect to the length of the spine. For "average width" is intended the mean diameter of a single spine.
	BPFilamentSplitBranchLevels.m	Split one filament object in different filaments. The branches directly connected to the root are first-level branches; The branches directly connected to the first-level branches are second-level branches; and so on. For each level, a new filament object, which collects the branches of the level, is created. The number of filaments created is equal to the maximal level of the branches of the original filament.
	BPFilamentSplitIntoBranches.m	Split one filament object in different filaments. The new filaments go from the root to a terminal of the original filament and they do not have branches. The number of filaments created is equal to the number of terminals of the original filament.

Tracks Functions

	BPTrackPlotAngles.m	Plot the angles of the track.
	BPTrackPlotDistanceBetweenTracks.m	Plot the distance between the selected track and the other visible tracks that are in the same group.
	BPTrackPlotLength.m	Plot the length of the track steps.
	BPTrackTranslate.m	Copy the tracks that are in the same group of the selected track. The copies are then translated so that they have the same starting point.

Surface Functions

	BPSurfaceMerge.m	Merge all the surface objects that are in the same folder in a single surface object.
	BPDistanceTransform.m ddist.m, ddist.dll	Create and compute a new channel, where the voxel intensity indicates the shortest distance to a surface object. Require ddist.m and ddist.dll.
	BPSpotsAndSurfacesDistance.m	Compute the distance between all the pairs of visible and valid objects that are in the same group. Valid objects are surfaces and spots. The center of a spots object is equal to the mean of the coordinates of all the single spots that belong to the object. The center of a surface object is an approximation of the center of mass of the object represented.

Camera Functions

	BPCameraFitToSelectedObject.m	Move the camera so that the selected object is centered in the window. The camera orientation is not modified. Apply to Spots, Surface, Track and Filament.
	BPCameraManager.m	Save/load/clear camera settings in .mat files. Settings are: Position, orientation, perspective, orthographic, focus and height.
	BPCameraSetAngle.m	The angle of the camera is defined using the [Azimuth, Elevation, Angle] coordinates. The camera is rotated around axis Y by Angle, then around axis X by Elevation, then around axis Y by Azimuth. Coordinates can be ambiguous: Different Azimuth, Elevation, Angle can determine the same camera orientation. The user can specify the coordinates through 3 sliders.

Stereology Functions

	BPStereologyBox.m	Create a surface object with the shape of a cube. The edge length is defined by the user.
	BPStereologySpaceBall.m	Create a surface object with the shape of a half sphere. The radius size is defined by the user.

Other Functions

	BPObjectManager.m	Save/load/clear single Imaris objects in .mat files. Apply to Spots, Surface, Track, Filament and Groups. Groups are saved with all their content. Only first-level objects (mSurpassScene direct childs) can be saved.
	BPGetImarisImage.m	Get and returns the Imaris DataSet. This function can be used as utility for other functions; It is not called directly by Imaris.
	BPSetImarisImage.m	Change the Imaris DataSet. This function can be used as utility for other functions; It is not called directly by Imaris.

• Setup with Imaris 5.7.0 and higher: A base set of XTensions is already installed with Imaris. Additional XTensions can be installed like before (copy them into the "XTensions" folder).
• Setup with Imaris 4.2.0 and higher: Copy the m-Files into a subfolder named "XTensions" of Imaris (e.g. C:\Program Files\Bitplane\Imaris 5\XTensions\). You may download ImarisXTensions1_4_2w.zip which contains all above files.
• Setup with Imaris 4.1.3: Download and run the ImarisXTensions 1.1.0. The installation program copies all the m-Files, adds the Matlab path and adjusts the Imaris menus. Make sure to install Matlab and Imaris first. The files can also be installed manually. Each of the above Imaris XTensions contains a description in it's header how it has to be installed for Imaris. In general they must be copied into a working directory of Matlab. Then start Imaris and open the tools preferences (edit / preferences / tools). Import this file to configure all custom menus, toolbars, and tabs at once.