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+diffgeometry
+project/@Experiment
+surfaceAnalysis/@SurfaceOfInterest
+surfaceDetection
+surfaceFitting
examples
external
generalfunctions
.gitignore
COPYING.txt
README.md
README.txt
UMLdiagram.pdf
UMLdiagram.uxf
setup.m

README.md

%% ImSAnE installation instructions

Copy the folder ImSAnE to wherever you want it. E.g. C:\ImSAnE in windows or /User/Shared/ImSAnE

Open setup.m in matlab and run each block with command + enter The last block contain settings that can be changed or left to their default.

%% MATLAB versions successfully tested:

Certain functions used require Matlab version 2012a or later. Tested combinations of Matlab and operating system sorted by Matlab version:

Matlab 2014a - Mac OS X 10.10.2

Matlab 2013a - Mac OS X 10.10.2 - Ubuntu LTS 12.04 & 14.04 - Windows 7 Professional

%% Bioformats to automatically read metadata

The reading of raw data assumes tif format and requires specification of number of channels by hand. To read more formats and detect some metadata automatically, one can download the bioformats package from

http://downloads.openmicroscopy.org/bio-formats/5.1.3/

and place the jar file in the folder external/bfmatlab