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@icaoberg
icaoberg / script.sh
Created April 29, 2015 12:48
Helper script that downloads and runs CellOrganizer v2.2 for MMBioS 2015
#!/bin/bash
wget -nc http://cellorganizer.org/Downloads/v2.0/cellorganizer_v2.2.zip
wget -nc http://cellorganizer.org/mmbios/2015/bafilModelsForMMBIOS.zip
wget -nc http://cellorganizer.org/mmbios/2015/cell1.xml
if [ -f cellorganizer_v2.2.zip ]; then
unzip -o cellorganizer_v2.2.zip
@icaoberg
icaoberg / script.sh
Last active August 29, 2015 14:17
Helper script that downloads the source and intermediate results for murphylab185
#!/bin/bash
echo "*********************"
echo "* LICENSE AGREEMENT *"
echo "*********************"
echo "All data downloaded from the Murphy Lab web site (http://murphylab.web.cmu.edu) remain the property of the
Murphy"
echo "Lab. You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the"
echo "following conditions: (a) you agree to include a reference to"
echo ""
@icaoberg
icaoberg / script.m
Last active August 29, 2015 14:16
Helper script that generates a library of png from a collection of multi tiffs
patterns = { 'nuc', 'endo', 'mit', 'lyso' };
for i=1:length(patterns)
pattern = patterns{i};
disp( pattern );
mkdir(pattern);
files = dir( '*.tif' );
for j=1:1:length(files)
file = files(j).name;
disp( [ 'Opening ' file ] );
@icaoberg
icaoberg / script.sh
Last active August 29, 2015 14:15
cellorganizer-demo3D12 public CI script #ubuntu #macosx #matlab #cellorganizer
###########################################
# REMEMBER TO SET UP THE VARIABLE $OPTION #
###########################################
find . -name "*lock*" -exec rm -f {} \;
OPTION=$1
echo "help demo3D12;
@icaoberg
icaoberg / script.sh
Created February 17, 2015 06:58
Helper script that downloads the 3D UCE dataset from the Murphy Lab at Carnegie Mellon University
#!/bin/bash
echo "*********************"
echo "* LICENSE AGREEMENT *"
echo "*********************"
echo "All data downloaded from the Murphy Lab web site (http://murphylab.web.cmu.edu) remain the property of the
Murphy"
echo "Lab. You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the"
echo "following conditions: (a) you agree to include a reference to"
echo ""
@icaoberg
icaoberg / script.sh
Created February 17, 2015 06:49
Helper script that downloads the hand-segmented 2D 3T3 and U20S nuclear images dataset from the Murphy Lab at Carnegie Mellon University
#!/bin/bash
echo "*********************"
echo "* LICENSE AGREEMENT *"
echo "*********************"
echo "All data downloaded from the Murphy Lab web site (http://murphylab.web.cmu.edu) remain the property of the
Murphy"
echo "Lab. You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the"
echo "following conditions: (a) you agree to include a reference to"
echo ""
@icaoberg
icaoberg / script.sh
Created February 17, 2015 06:43
Helper script that downloads the 2D CHO dataset from the Murphy Lab at Carnegie Mellon University
#!/bin/bash
echo "*********************"
echo "* LICENSE AGREEMENT *"
echo "*********************"
echo "All data downloaded from the Murphy Lab web site (http://murphylab.web.cmu.edu) remain the property of the
Murphy"
echo "Lab. You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the"
echo "following conditions: (a) you agree to include a reference to"
echo ""
@icaoberg
icaoberg / script.sh
Created February 17, 2015 06:32
Helper script that downloads the 3D HeLa multi-tiff dataset from the Murphy Lab at Carnegie Mellon University
#!/bin/bash
echo "*********************"
echo "* LICENSE AGREEMENT *"
echo "*********************"
echo "All data downloaded from the Murphy Lab web site (http://murphylab.web.cmu.edu) remain the property of the
Murphy"
echo "Lab. You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the"
echo "following conditions: (a) you agree to include a reference to"
echo ""
@icaoberg
icaoberg / script.sh
Last active August 29, 2015 14:15
Helper script that downloads the 2D 3T3 RandTag Set 4 dataset from the Murphy Lab at Carnegie Mellon University
#!/bin/bash
echo "*********************"
echo "* LICENSE AGREEMENT *"
echo "*********************"
echo "All data downloaded from the Murphy Lab web site (http://murphylab.web.cmu.edu) remain the property of the
Murphy"
echo "Lab. You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the"
echo "following conditions: (a) you agree to include a reference to"
echo ""
@icaoberg
icaoberg / script.sh
Last active August 29, 2015 14:15
Helper script that downloads the 2D 3T3 RandTag Set 3 dataset from the Murphy Lab at Carnegie Mellon University
#!/bin/bash
echo "*********************"
echo "* LICENSE AGREEMENT *"
echo "*********************"
echo "All data downloaded from the Murphy Lab web site (http://murphylab.web.cmu.edu) remain the property of the
Murphy"
echo "Lab. You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the"
echo "following conditions: (a) you agree to include a reference to"
echo ""