Maté Biro - Immune Atlas

Immune Atlas

Immune Atlas is a plugin (XTension) for Imaris (Bitplane) written in MATLAB that enables

the calculation of the nearest distance from cells to the vasculature.

All this seamlessly in 3-Dimensions and from within the Imaris platform.

The Immune Atlas plugin is now at version 2.0, and is now fully integrated with Imaris.

Download the Immune Atlas: Cells to Vasculature Nearest Distance plugin version 2.0.

Fill out the short form to obtain the download consisting of a Zip file called ImmuneAtlas.zip, containing 2 files (ImmuneAtlasCell2VasculatureNearestDistance.m and ImmuneAtlasLogo.jpg), which both need to reside in the same directory, the path to which has to be added to the CustomTools section of the Preferences in Imaris.

The following publication should be referenced upon use:

Tong P.L., Roediger B., Kolesnikoff N., Biro M., Tay S.S., Jain R., Shaw L.E., Grimbaldeston M.A., Weninger W. (2014)

The skin immune atlas: three-dimensional analysis of cutaneous leukocyte subsets by multiphoton microscopy

Journal of Investigative Dermatology (In press: doi: 10.1038/jid.2014.289)

For more information about how to install and run XTensions in Imaris, please refer to:

The Bitplane tutorial on how to enable ImageJ/Fiji and MATLAB plugins in Imaris.
The Imaris Reference Manual accessible via the Help menu in Imaris.
The Imaris Open forum at http://open.bitplane.com.

Plugin instructions:

First, cells from which nearest distances are to be calculated need to be assigned Spots objects, and the vasculature a Surface object in Imaris.
The plugin can then be called from the Image Processing menu, or within the custom tools tab of Spots, Surfaces or Group items in the Surpass Scene tree.
The plugin calculates the nearest distance from each Spot (or cell) to the Surface (vasculature) and creates a new Statistics field for the Spots called "Nearest Distance to SurfaceName", where SurfaceName is the name of the Surface object representing the vasculature.
An option, selectable via a pop-up dialog, allows for the creation of a Group of Measurement Points. If selected, a pair of Measurement Points is created for each Spot representing a cell: one at the position of the cell (called Spot) and one at the corresponding nearest point on the vasculature (called Surf). Following creation of the Measurement Points, nearest distances are displayed in the Imaris Surpass Scene. Display options for each point can be set.
In addition to the newly created Nearest Distance statistics for each Spot, the Measurement Points group also has fully enabled statistics, thus allowing for access to the exact 3D coordinates of the nearest points on the vasculature, intensities at each point in the various channels etc. All these statistics are fully exportable to Microsoft Excel, CSV or xml formats from Imaris.

Historically, the Spots objects representing the position of the cells and the Surface object representing the volume occupied by the vasculature were exported to and rendered in Matlab, following which numerical data was automatically saved into a CSV file in the original folder, together with the Matlab 3D figure.

Immune Atlas was developed in MATLAB® (The MathWorks, Inc., Natick, MA) and runs embedded in Imaris (Bitplane, Zurich, Switzerland) under any operating system supporting MATLAB and Imaris, notably Windows and Mac OS X.

Immune Atlas is freely available for non-commercial use under the GNU General Public License.

Immune Atlas is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Immune Atlas is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

The Immune Atlas logo made use of an image of a T lymphocyte (credit: National Institute of Allergy and Infectious Disease, Licence ) as well as a vectorised globe/map from VECTORTEMPLATES.com

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