GitHub - rolandmas/threeB: Bayesian analysis of blinking and bleaching

ThreeB

This is the software for 3B microscopy analysis.

For information on using the software, please refer to the documentation (in the html/ directory) or http://www.coxphysics.com/3b/index.html

If you want to try or test the software, then the recomended method is to use a release of the ImageJ plugin (which supports Windows and Linux). If you want more control or to run on a cluster, then the recommended method is to use a precompiled binary from the most recent release.

If you download a precompiled executable for a cluster, you will still need the multispot5.cfg configuration file from this repository.

Relseaes

http://www.coxphysics.com/3b/3B_releases/

Building the static executables

The easiest and fastest way is using docker, so you need to get docker. Then go into your source directory and run:

docker run -v $PWD:/home/build edrosten/threeb-static-build-env ./configure
docker run -v $PWD:/home/build edrosten/threeb-static-build-env make multispot5_static -j 8

Building the plugin (and static executables)

This is the "classic" way of building 3B, and I haven't ported this over to docker yet. It does more or less the same thing, but predates docker by about 6 years or so, so you need sudo access.

You will need a Linux machine. On ubuntu or debian, run:

sudo apt install debootstrap
sudo bash build_plugin.sh

sudo access is needed since the script runs debootstrap which is used to make some clean, consistent debian environments for a repeatable build.

Building completely by hand

Don't do this unless you are really very confident and 100% sure you need it.

Building the is done the usual way (./configure && make), but that's a little tricky these days because (1) building static binaries is quite hard and (2) I wrote this in 2009 and released it in 2011, so it doesn't currently build on new systems with up to date library versions.

The usual ./configure && make can be used to build the software. The software depends on:

TooN http://www.edwardrosten.com/cvd/toon.html libcvd http://www.edwardrosten.com/cvd/ gvars3 http://www.edwardrosten.com/cvd/gvars3.html

You currently need old versions (newer ones will work, but not too new)

http://www.edwardrosten.com/cvd/libcvd-20121025.tar.gz http://www.edwardrosten.com/cvd/gvars-3.0.tar.gz http://www.edwardrosten.com/cvd/TooN-2.0.tar.gz

You'll likely need an old compiler as well. The static executables will build with gcc-4.4.3. If you want to build the plugin, you'll need a newer MinGW environment. Building for MinGW is hard and requires patching then building dependencies.

License

The software may be redistributed under the terms of the GPL 3.0

ThreeB

This is the software for 3B microscopy analysis.

For information on using the software, please refer to the documentation (in the html/ directory) or http://www.coxphysics.com/3b/index.html

If you want to try or test the software, then the recomended method is to use a release of the ImageJ plugin (which supports Windows and Linux). If you want more control or to run on a cluster, then the recommended method is to use a precompiled binary from the most recent release.

If you download a precompiled executable for a cluster, you will still need the multispot5.cfg configuration file from this repository.

Relseaes

http://www.coxphysics.com/3b/3B_releases/

Building the static executables

The easiest and fastest way is using docker, so you need to get docker. Then go into your source directory and run:

docker run -v $PWD:/home/build edrosten/threeb-static-build-env ./configure
docker run -v $PWD:/home/build edrosten/threeb-static-build-env make multispot5_static -j 8

Building the plugin (and static executables)

This is the "classic" way of building 3B, and I haven't ported this over to docker yet. It does more or less the same thing, but predates docker by about 6 years or so, so you need sudo access.

You will need a Linux machine. On ubuntu or debian, run:

sudo apt install debootstrap
sudo bash build_plugin.sh

sudo access is needed since the script runs debootstrap which is used to make some clean, consistent debian environments for a repeatable build.

Building completely by hand

Don't do this unless you are really very confident and 100% sure you need it.

Building the is done the usual way (./configure && make), but that's a little tricky these days because (1) building static binaries is quite hard and (2) I wrote this in 2009 and released it in 2011, so it doesn't currently build on new systems with up to date library versions.

The usual ./configure && make can be used to build the software. The software depends on:

TooN http://www.edwardrosten.com/cvd/toon.html libcvd http://www.edwardrosten.com/cvd/ gvars3 http://www.edwardrosten.com/cvd/gvars3.html

You currently need old versions (newer ones will work, but not too new)

http://www.edwardrosten.com/cvd/libcvd-20121025.tar.gz http://www.edwardrosten.com/cvd/gvars-3.0.tar.gz http://www.edwardrosten.com/cvd/TooN-2.0.tar.gz

You'll likely need an old compiler as well. The static executables will build with gcc-4.4.3. If you want to build the plugin, you'll need a newer MinGW environment. Building for MinGW is hard and requires patching then building dependencies.

License

The software may be redistributed under the terms of the GPL 3.0

ThreeB

This is the software for 3B microscopy analysis.

For information on using the software, please refer to the documentation (in the html/ directory) or http://www.coxphysics.com/3b/index.html

If you want to try or test the software, then the recomended method is to use a release of the ImageJ plugin (which supports Windows and Linux). If you want more control or to run on a cluster, then the recommended method is to use a precompiled binary from the most recent release.

If you download a precompiled executable for a cluster, you will still need the multispot5.cfg configuration file from this repository.

Relseaes

http://www.coxphysics.com/3b/3B_releases/

Building the static executables

The easiest and fastest way is using docker, so you need to get docker. Then go into your source directory and run:

docker run -v $PWD:/home/build edrosten/threeb-static-build-env ./configure
docker run -v $PWD:/home/build edrosten/threeb-static-build-env make multispot5_static -j 8

Building the plugin (and static executables)

This is the "classic" way of building 3B, and I haven't ported this over to docker yet. It does more or less the same thing, but predates docker by about 6 years or so, so you need sudo access.

You will need a Linux machine. On ubuntu or debian, run:

sudo apt install debootstrap
sudo bash build_plugin.sh

sudo access is needed since the script runs debootstrap which is used to make some clean, consistent debian environments for a repeatable build.

Building completely by hand

Don't do this unless you are really very confident and 100% sure you need it.

Building the is done the usual way (./configure && make), but that's a little tricky these days because (1) building static binaries is quite hard and (2) I wrote this in 2009 and released it in 2011, so it doesn't currently build on new systems with up to date library versions.

The usual ./configure && make can be used to build the software. The software depends on:

TooN http://www.edwardrosten.com/cvd/toon.html libcvd http://www.edwardrosten.com/cvd/ gvars3 http://www.edwardrosten.com/cvd/gvars3.html

You currently need old versions (newer ones will work, but not too new)

http://www.edwardrosten.com/cvd/libcvd-20121025.tar.gz http://www.edwardrosten.com/cvd/gvars-3.0.tar.gz http://www.edwardrosten.com/cvd/TooN-2.0.tar.gz

You'll likely need an old compiler as well. The static executables will build with gcc-4.4.3. If you want to build the plugin, you'll need a newer MinGW environment. Building for MinGW is hard and requires patching then building dependencies.

License

The software may be redistributed under the terms of the GPL 3.0

ThreeB

This is the software for 3B microscopy analysis.

For information on using the software, please refer to the documentation (in the html/ directory) or http://www.coxphysics.com/3b/index.html

If you want to try or test the software, then the recomended method is to use a release of the ImageJ plugin (which supports Windows and Linux). If you want more control or to run on a cluster, then the recommended method is to use a precompiled binary from the most recent release.

If you download a precompiled executable for a cluster, you will still need the multispot5.cfg configuration file from this repository.

Relseaes

http://www.coxphysics.com/3b/3B_releases/

Building the static executables

The easiest and fastest way is using docker, so you need to get docker. Then go into your source directory and run:

docker run -v $PWD:/home/build edrosten/threeb-static-build-env ./configure
docker run -v $PWD:/home/build edrosten/threeb-static-build-env make multispot5_static -j 8

Building the plugin (and static executables)

This is the "classic" way of building 3B, and I haven't ported this over to docker yet. It does more or less the same thing, but predates docker by about 6 years or so, so you need sudo access.

You will need a Linux machine. On ubuntu or debian, run:

sudo apt install debootstrap
sudo bash build_plugin.sh

sudo access is needed since the script runs debootstrap which is used to make some clean, consistent debian environments for a repeatable build.

Building completely by hand

Don't do this unless you are really very confident and 100% sure you need it.

Building the is done the usual way (./configure && make), but that's a little tricky these days because (1) building static binaries is quite hard and (2) I wrote this in 2009 and released it in 2011, so it doesn't currently build on new systems with up to date library versions.

The usual ./configure && make can be used to build the software. The software depends on:

TooN http://www.edwardrosten.com/cvd/toon.html libcvd http://www.edwardrosten.com/cvd/ gvars3 http://www.edwardrosten.com/cvd/gvars3.html

You currently need old versions (newer ones will work, but not too new)

http://www.edwardrosten.com/cvd/libcvd-20121025.tar.gz http://www.edwardrosten.com/cvd/gvars-3.0.tar.gz http://www.edwardrosten.com/cvd/TooN-2.0.tar.gz

You'll likely need an old compiler as well. The static executables will build with gcc-4.4.3. If you want to build the plugin, you'll need a newer MinGW environment. Building for MinGW is hard and requires patching then building dependencies.

License

The software may be redistributed under the terms of the GPL 3.0

ThreeB

This is the software for 3B microscopy analysis.

For information on using the software, please refer to the documentation (in the html/ directory) or http://www.coxphysics.com/3b/index.html

If you want to try or test the software, then the recomended method is to use a release of the ImageJ plugin (which supports Windows and Linux). If you want more control or to run on a cluster, then the recommended method is to use a precompiled binary from the most recent release.

If you download a precompiled executable for a cluster, you will still need the multispot5.cfg configuration file from this repository.

Relseaes

http://www.coxphysics.com/3b/3B_releases/

Building the static executables

The easiest and fastest way is using docker, so you need to get docker. Then go into your source directory and run:

docker run -v $PWD:/home/build edrosten/threeb-static-build-env ./configure
docker run -v $PWD:/home/build edrosten/threeb-static-build-env make multispot5_static -j 8

Building the plugin (and static executables)

This is the "classic" way of building 3B, and I haven't ported this over to docker yet. It does more or less the same thing, but predates docker by about 6 years or so, so you need sudo access.

You will need a Linux machine. On ubuntu or debian, run:

sudo apt install debootstrap
sudo bash build_plugin.sh

sudo access is needed since the script runs debootstrap which is used to make some clean, consistent debian environments for a repeatable build.

Building completely by hand

Don't do this unless you are really very confident and 100% sure you need it.

Building the is done the usual way (./configure && make), but that's a little tricky these days because (1) building static binaries is quite hard and (2) I wrote this in 2009 and released it in 2011, so it doesn't currently build on new systems with up to date library versions.

The usual ./configure && make can be used to build the software. The software depends on:

TooN http://www.edwardrosten.com/cvd/toon.html libcvd http://www.edwardrosten.com/cvd/ gvars3 http://www.edwardrosten.com/cvd/gvars3.html

You currently need old versions (newer ones will work, but not too new)

http://www.edwardrosten.com/cvd/libcvd-20121025.tar.gz http://www.edwardrosten.com/cvd/gvars-3.0.tar.gz http://www.edwardrosten.com/cvd/TooN-2.0.tar.gz

You'll likely need an old compiler as well. The static executables will build with gcc-4.4.3. If you want to build the plugin, you'll need a newer MinGW environment. Building for MinGW is hard and requires patching then building dependencies.

License

The software may be redistributed under the terms of the GPL 3.0

ThreeB

This is the software for 3B microscopy analysis.

For information on using the software, please refer to the documentation (in the html/ directory) or http://www.coxphysics.com/3b/index.html

If you want to try or test the software, then the recomended method is to use a release of the ImageJ plugin (which supports Windows and Linux). If you want more control or to run on a cluster, then the recommended method is to use a precompiled binary from the most recent release.

If you download a precompiled executable for a cluster, you will still need the multispot5.cfg configuration file from this repository.

Relseaes

http://www.coxphysics.com/3b/3B_releases/

Building the static executables

The easiest and fastest way is using docker, so you need to get docker. Then go into your source directory and run:

docker run -v $PWD:/home/build edrosten/threeb-static-build-env ./configure
docker run -v $PWD:/home/build edrosten/threeb-static-build-env make multispot5_static -j 8

Building the plugin (and static executables)

This is the "classic" way of building 3B, and I haven't ported this over to docker yet. It does more or less the same thing, but predates docker by about 6 years or so, so you need sudo access.

You will need a Linux machine. On ubuntu or debian, run:

sudo apt install debootstrap
sudo bash build_plugin.sh

sudo access is needed since the script runs debootstrap which is used to make some clean, consistent debian environments for a repeatable build.

Building completely by hand

Don't do this unless you are really very confident and 100% sure you need it.

Building the is done the usual way (./configure && make), but that's a little tricky these days because (1) building static binaries is quite hard and (2) I wrote this in 2009 and released it in 2011, so it doesn't currently build on new systems with up to date library versions.

The usual ./configure && make can be used to build the software. The software depends on:

TooN http://www.edwardrosten.com/cvd/toon.html libcvd http://www.edwardrosten.com/cvd/ gvars3 http://www.edwardrosten.com/cvd/gvars3.html

You currently need old versions (newer ones will work, but not too new)

http://www.edwardrosten.com/cvd/libcvd-20121025.tar.gz http://www.edwardrosten.com/cvd/gvars-3.0.tar.gz http://www.edwardrosten.com/cvd/TooN-2.0.tar.gz

You'll likely need an old compiler as well. The static executables will build with gcc-4.4.3. If you want to build the plugin, you'll need a newer MinGW environment. Building for MinGW is hard and requires patching then building dependencies.

License

The software may be redistributed under the terms of the GPL 3.0

ThreeB

This is the software for 3B microscopy analysis.

For information on using the software, please refer to the documentation (in the html/ directory) or http://www.coxphysics.com/3b/index.html

If you want to try or test the software, then the recomended method is to use a release of the ImageJ plugin (which supports Windows and Linux). If you want more control or to run on a cluster, then the recommended method is to use a precompiled binary from the most recent release.

If you download a precompiled executable for a cluster, you will still need the multispot5.cfg configuration file from this repository.

Relseaes

http://www.coxphysics.com/3b/3B_releases/

Building the static executables

The easiest and fastest way is using docker, so you need to get docker. Then go into your source directory and run:

docker run -v $PWD:/home/build edrosten/threeb-static-build-env ./configure
docker run -v $PWD:/home/build edrosten/threeb-static-build-env make multispot5_static -j 8

Building the plugin (and static executables)

This is the "classic" way of building 3B, and I haven't ported this over to docker yet. It does more or less the same thing, but predates docker by about 6 years or so, so you need sudo access.

You will need a Linux machine. On ubuntu or debian, run:

sudo apt install debootstrap
sudo bash build_plugin.sh

sudo access is needed since the script runs debootstrap which is used to make some clean, consistent debian environments for a repeatable build.

Building completely by hand

Don't do this unless you are really very confident and 100% sure you need it.

Building the is done the usual way (./configure && make), but that's a little tricky these days because (1) building static binaries is quite hard and (2) I wrote this in 2009 and released it in 2011, so it doesn't currently build on new systems with up to date library versions.

The usual ./configure && make can be used to build the software. The software depends on:

TooN http://www.edwardrosten.com/cvd/toon.html libcvd http://www.edwardrosten.com/cvd/ gvars3 http://www.edwardrosten.com/cvd/gvars3.html

You currently need old versions (newer ones will work, but not too new)

http://www.edwardrosten.com/cvd/libcvd-20121025.tar.gz http://www.edwardrosten.com/cvd/gvars-3.0.tar.gz http://www.edwardrosten.com/cvd/TooN-2.0.tar.gz

You'll likely need an old compiler as well. The static executables will build with gcc-4.4.3. If you want to build the plugin, you'll need a newer MinGW environment. Building for MinGW is hard and requires patching then building dependencies.

License

The software may be redistributed under the terms of the GPL 3.0

ThreeB

This is the software for 3B microscopy analysis.

For information on using the software, please refer to the documentation (in the html/ directory) or http://www.coxphysics.com/3b/index.html

If you want to try or test the software, then the recomended method is to use a release of the ImageJ plugin (which supports Windows and Linux). If you want more control or to run on a cluster, then the recommended method is to use a precompiled binary from the most recent release.

If you download a precompiled executable for a cluster, you will still need the multispot5.cfg configuration file from this repository.

Relseaes

http://www.coxphysics.com/3b/3B_releases/

Building the static executables

The easiest and fastest way is using docker, so you need to get docker. Then go into your source directory and run:

docker run -v $PWD:/home/build edrosten/threeb-static-build-env ./configure
docker run -v $PWD:/home/build edrosten/threeb-static-build-env make multispot5_static -j 8

Building the plugin (and static executables)

This is the "classic" way of building 3B, and I haven't ported this over to docker yet. It does more or less the same thing, but predates docker by about 6 years or so, so you need sudo access.

You will need a Linux machine. On ubuntu or debian, run:

sudo apt install debootstrap
sudo bash build_plugin.sh

sudo access is needed since the script runs debootstrap which is used to make some clean, consistent debian environments for a repeatable build.

Building completely by hand

Don't do this unless you are really very confident and 100% sure you need it.

Building the is done the usual way (./configure && make), but that's a little tricky these days because (1) building static binaries is quite hard and (2) I wrote this in 2009 and released it in 2011, so it doesn't currently build on new systems with up to date library versions.

The usual ./configure && make can be used to build the software. The software depends on:

TooN http://www.edwardrosten.com/cvd/toon.html libcvd http://www.edwardrosten.com/cvd/ gvars3 http://www.edwardrosten.com/cvd/gvars3.html

You currently need old versions (newer ones will work, but not too new)

http://www.edwardrosten.com/cvd/libcvd-20121025.tar.gz http://www.edwardrosten.com/cvd/gvars-3.0.tar.gz http://www.edwardrosten.com/cvd/TooN-2.0.tar.gz

You'll likely need an old compiler as well. The static executables will build with gcc-4.4.3. If you want to build the plugin, you'll need a newer MinGW environment. Building for MinGW is hard and requires patching then building dependencies.

License

The software may be redistributed under the terms of the GPL 3.0

Name		Name	Last commit message	Last commit date
docker		docker
jar		jar
tag		tag
.gitignore		.gitignore
CHANGES-1.2		CHANGES-1.2
CREDITS		CREDITS
ClassicGlow.java		ClassicGlow.java
Doxyfile		Doxyfile
HEAD		HEAD
LICENSE		LICENSE
LoadTestData.java		LoadTestData.java
Makefile.in		Makefile.in
QuickPalmLoader.java		QuickPalmLoader.java
README.md		README.md
TODO		TODO
ThreeBHelp.java		ThreeBHelp.java
ThreeBLoader.java		ThreeBLoader.java
build_3b.sh		build_3b.sh
build_and_install.sh		build_and_install.sh
build_plugin.sh		build_plugin.sh
clapack_mingw.patch		clapack_mingw.patch
config		config
configure		configure
configure.ac		configure.ac
conjugate_gradient_only.h		conjugate_gradient_only.h
debug.cc		debug.cc
debug.h		debug.h
description		description
documentation.h		documentation.h
drift.h		drift.h
forward_algorithm.h		forward_algorithm.h
forward_filtering_backwards_sampling.cc		forward_filtering_backwards_sampling.cc
get_all_spots.awk		get_all_spots.awk
header.txt		header.txt
make_grid_markup.cc		make_grid_markup.cc
makedist.sh		makedist.sh
mersenne.cpp		mersenne.cpp
mt19937.h		mt19937.h
multispot5.cc		multispot5.cc
multispot5.cfg		multispot5.cfg
multispot5.h		multispot5.h
multispot5_gui.cc		multispot5_gui.cc
multispot5_headless.cc		multispot5_headless.cc
multispot5_jni.cc		multispot5_jni.cc
multispot5_place_choice.cc		multispot5_place_choice.cc
multispot5_place_choice.h		multispot5_place_choice.h
multispot5_place_methods.cc		multispot5_place_methods.cc
multispot5_place_methods.h		multispot5_place_methods.h
numerical_derivatives.h		numerical_derivatives.h
poisson.cc		poisson.cc
poisson.h		poisson.h
randomc.h		randomc.h
sampled_multispot.h		sampled_multispot.h
second.c		second.c
setup_build_env.sh		setup_build_env.sh
spot_viewer.cc		spot_viewer.cc
spot_viewer.cfg		spot_viewer.cfg
spot_with_background.hh		spot_with_background.hh
storm.h		storm.h
storm.sty		storm.sty
storm_imagery.cc		storm_imagery.cc
storm_imagery.h		storm_imagery.h
storm_imagery_no_load.cc		storm_imagery_no_load.cc
test_forward_algorithm.cc		test_forward_algorithm.cc
test_forward_backward.cc		test_forward_backward.cc
test_forward_backward_deriv.cc		test_forward_backward_deriv.cc
three_B.java		three_B.java
utility.cc		utility.cc
utility.h		utility.h
version.cc		version.cc

Name		Name	Last commit message	Last commit date
docker		docker
jar		jar
tag		tag
.gitignore		.gitignore
CHANGES-1.2		CHANGES-1.2
CREDITS		CREDITS
ClassicGlow.java		ClassicGlow.java
Doxyfile		Doxyfile
HEAD		HEAD
LICENSE		LICENSE
LoadTestData.java		LoadTestData.java
Makefile.in		Makefile.in
QuickPalmLoader.java		QuickPalmLoader.java
README.md		README.md
TODO		TODO
ThreeBHelp.java		ThreeBHelp.java
ThreeBLoader.java		ThreeBLoader.java
build_3b.sh		build_3b.sh
build_and_install.sh		build_and_install.sh
build_plugin.sh		build_plugin.sh
clapack_mingw.patch		clapack_mingw.patch
config		config
configure		configure
configure.ac		configure.ac
conjugate_gradient_only.h		conjugate_gradient_only.h
debug.cc		debug.cc
debug.h		debug.h
description		description
documentation.h		documentation.h
drift.h		drift.h
forward_algorithm.h		forward_algorithm.h
forward_filtering_backwards_sampling.cc		forward_filtering_backwards_sampling.cc
get_all_spots.awk		get_all_spots.awk
header.txt		header.txt
make_grid_markup.cc		make_grid_markup.cc
makedist.sh		makedist.sh
mersenne.cpp		mersenne.cpp
mt19937.h		mt19937.h
multispot5.cc		multispot5.cc
multispot5.cfg		multispot5.cfg
multispot5.h		multispot5.h
multispot5_gui.cc		multispot5_gui.cc
multispot5_headless.cc		multispot5_headless.cc
multispot5_jni.cc		multispot5_jni.cc
multispot5_place_choice.cc		multispot5_place_choice.cc
multispot5_place_choice.h		multispot5_place_choice.h
multispot5_place_methods.cc		multispot5_place_methods.cc
multispot5_place_methods.h		multispot5_place_methods.h
numerical_derivatives.h		numerical_derivatives.h
poisson.cc		poisson.cc
poisson.h		poisson.h
randomc.h		randomc.h
sampled_multispot.h		sampled_multispot.h
second.c		second.c
setup_build_env.sh		setup_build_env.sh
spot_viewer.cc		spot_viewer.cc
spot_viewer.cfg		spot_viewer.cfg
spot_with_background.hh		spot_with_background.hh
storm.h		storm.h
storm.sty		storm.sty
storm_imagery.cc		storm_imagery.cc
storm_imagery.h		storm_imagery.h
storm_imagery_no_load.cc		storm_imagery_no_load.cc
test_forward_algorithm.cc		test_forward_algorithm.cc
test_forward_backward.cc		test_forward_backward.cc
test_forward_backward_deriv.cc		test_forward_backward_deriv.cc
three_B.java		three_B.java
utility.cc		utility.cc
utility.h		utility.h
version.cc		version.cc

Name		Name	Last commit message	Last commit date
docker		docker
jar		jar
tag		tag
.gitignore		.gitignore
CHANGES-1.2		CHANGES-1.2
CREDITS		CREDITS
ClassicGlow.java		ClassicGlow.java
Doxyfile		Doxyfile
HEAD		HEAD
LICENSE		LICENSE
LoadTestData.java		LoadTestData.java
Makefile.in		Makefile.in
QuickPalmLoader.java		QuickPalmLoader.java
README.md		README.md
TODO		TODO
ThreeBHelp.java		ThreeBHelp.java
ThreeBLoader.java		ThreeBLoader.java
build_3b.sh		build_3b.sh
build_and_install.sh		build_and_install.sh
build_plugin.sh		build_plugin.sh
clapack_mingw.patch		clapack_mingw.patch
config		config
configure		configure
configure.ac		configure.ac
conjugate_gradient_only.h		conjugate_gradient_only.h
debug.cc		debug.cc
debug.h		debug.h
description		description
documentation.h		documentation.h
drift.h		drift.h
forward_algorithm.h		forward_algorithm.h
forward_filtering_backwards_sampling.cc		forward_filtering_backwards_sampling.cc
get_all_spots.awk		get_all_spots.awk
header.txt		header.txt
make_grid_markup.cc		make_grid_markup.cc
makedist.sh		makedist.sh
mersenne.cpp		mersenne.cpp
mt19937.h		mt19937.h
multispot5.cc		multispot5.cc
multispot5.cfg		multispot5.cfg
multispot5.h		multispot5.h
multispot5_gui.cc		multispot5_gui.cc
multispot5_headless.cc		multispot5_headless.cc
multispot5_jni.cc		multispot5_jni.cc
multispot5_place_choice.cc		multispot5_place_choice.cc
multispot5_place_choice.h		multispot5_place_choice.h
multispot5_place_methods.cc		multispot5_place_methods.cc
multispot5_place_methods.h		multispot5_place_methods.h
numerical_derivatives.h		numerical_derivatives.h
poisson.cc		poisson.cc
poisson.h		poisson.h
randomc.h		randomc.h
sampled_multispot.h		sampled_multispot.h
second.c		second.c
setup_build_env.sh		setup_build_env.sh
spot_viewer.cc		spot_viewer.cc
spot_viewer.cfg		spot_viewer.cfg
spot_with_background.hh		spot_with_background.hh
storm.h		storm.h
storm.sty		storm.sty
storm_imagery.cc		storm_imagery.cc
storm_imagery.h		storm_imagery.h
storm_imagery_no_load.cc		storm_imagery_no_load.cc
test_forward_algorithm.cc		test_forward_algorithm.cc
test_forward_backward.cc		test_forward_backward.cc
test_forward_backward_deriv.cc		test_forward_backward_deriv.cc
three_B.java		three_B.java
utility.cc		utility.cc
utility.h		utility.h
version.cc		version.cc

Name		Name	Last commit message	Last commit date
docker		docker
jar		jar
tag		tag
.gitignore		.gitignore
CHANGES-1.2		CHANGES-1.2
CREDITS		CREDITS
ClassicGlow.java		ClassicGlow.java
Doxyfile		Doxyfile
HEAD		HEAD
LICENSE		LICENSE
LoadTestData.java		LoadTestData.java
Makefile.in		Makefile.in
QuickPalmLoader.java		QuickPalmLoader.java
README.md		README.md
TODO		TODO
ThreeBHelp.java		ThreeBHelp.java
ThreeBLoader.java		ThreeBLoader.java
build_3b.sh		build_3b.sh
build_and_install.sh		build_and_install.sh
build_plugin.sh		build_plugin.sh
clapack_mingw.patch		clapack_mingw.patch
config		config
configure		configure
configure.ac		configure.ac
conjugate_gradient_only.h		conjugate_gradient_only.h
debug.cc		debug.cc
debug.h		debug.h
description		description
documentation.h		documentation.h
drift.h		drift.h
forward_algorithm.h		forward_algorithm.h
forward_filtering_backwards_sampling.cc		forward_filtering_backwards_sampling.cc
get_all_spots.awk		get_all_spots.awk
header.txt		header.txt
make_grid_markup.cc		make_grid_markup.cc
makedist.sh		makedist.sh
mersenne.cpp		mersenne.cpp
mt19937.h		mt19937.h
multispot5.cc		multispot5.cc
multispot5.cfg		multispot5.cfg
multispot5.h		multispot5.h
multispot5_gui.cc		multispot5_gui.cc
multispot5_headless.cc		multispot5_headless.cc
multispot5_jni.cc		multispot5_jni.cc
multispot5_place_choice.cc		multispot5_place_choice.cc
multispot5_place_choice.h		multispot5_place_choice.h
multispot5_place_methods.cc		multispot5_place_methods.cc
multispot5_place_methods.h		multispot5_place_methods.h
numerical_derivatives.h		numerical_derivatives.h
poisson.cc		poisson.cc
poisson.h		poisson.h
randomc.h		randomc.h
sampled_multispot.h		sampled_multispot.h
second.c		second.c
setup_build_env.sh		setup_build_env.sh
spot_viewer.cc		spot_viewer.cc
spot_viewer.cfg		spot_viewer.cfg
spot_with_background.hh		spot_with_background.hh
storm.h		storm.h
storm.sty		storm.sty
storm_imagery.cc		storm_imagery.cc
storm_imagery.h		storm_imagery.h
storm_imagery_no_load.cc		storm_imagery_no_load.cc
test_forward_algorithm.cc		test_forward_algorithm.cc
test_forward_backward.cc		test_forward_backward.cc
test_forward_backward_deriv.cc		test_forward_backward_deriv.cc
three_B.java		three_B.java
utility.cc		utility.cc
utility.h		utility.h
version.cc		version.cc

Name		Name	Last commit message	Last commit date
docker		docker
jar		jar
tag		tag
.gitignore		.gitignore
CHANGES-1.2		CHANGES-1.2
CREDITS		CREDITS
ClassicGlow.java		ClassicGlow.java
Doxyfile		Doxyfile
HEAD		HEAD
LICENSE		LICENSE
LoadTestData.java		LoadTestData.java
Makefile.in		Makefile.in
QuickPalmLoader.java		QuickPalmLoader.java
README.md		README.md
TODO		TODO
ThreeBHelp.java		ThreeBHelp.java
ThreeBLoader.java		ThreeBLoader.java
build_3b.sh		build_3b.sh
build_and_install.sh		build_and_install.sh
build_plugin.sh		build_plugin.sh
clapack_mingw.patch		clapack_mingw.patch
config		config
configure		configure
configure.ac		configure.ac
conjugate_gradient_only.h		conjugate_gradient_only.h
debug.cc		debug.cc
debug.h		debug.h
description		description
documentation.h		documentation.h
drift.h		drift.h
forward_algorithm.h		forward_algorithm.h
forward_filtering_backwards_sampling.cc		forward_filtering_backwards_sampling.cc
get_all_spots.awk		get_all_spots.awk
header.txt		header.txt
make_grid_markup.cc		make_grid_markup.cc
makedist.sh		makedist.sh
mersenne.cpp		mersenne.cpp
mt19937.h		mt19937.h
multispot5.cc		multispot5.cc
multispot5.cfg		multispot5.cfg
multispot5.h		multispot5.h
multispot5_gui.cc		multispot5_gui.cc
multispot5_headless.cc		multispot5_headless.cc
multispot5_jni.cc		multispot5_jni.cc
multispot5_place_choice.cc		multispot5_place_choice.cc
multispot5_place_choice.h		multispot5_place_choice.h
multispot5_place_methods.cc		multispot5_place_methods.cc
multispot5_place_methods.h		multispot5_place_methods.h
numerical_derivatives.h		numerical_derivatives.h
poisson.cc		poisson.cc
poisson.h		poisson.h
randomc.h		randomc.h
sampled_multispot.h		sampled_multispot.h
second.c		second.c
setup_build_env.sh		setup_build_env.sh
spot_viewer.cc		spot_viewer.cc
spot_viewer.cfg		spot_viewer.cfg
spot_with_background.hh		spot_with_background.hh
storm.h		storm.h
storm.sty		storm.sty
storm_imagery.cc		storm_imagery.cc
storm_imagery.h		storm_imagery.h
storm_imagery_no_load.cc		storm_imagery_no_load.cc
test_forward_algorithm.cc		test_forward_algorithm.cc
test_forward_backward.cc		test_forward_backward.cc
test_forward_backward_deriv.cc		test_forward_backward_deriv.cc
three_B.java		three_B.java
utility.cc		utility.cc
utility.h		utility.h
version.cc		version.cc

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