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.
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. For more information about how to install and run XTensions in Imaris, please refer to:
Plugin instructions:
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. Historical XTension available upon request. 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)
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 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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