Track points and cells on 2D tissues over time.
Project description
Point Tracker
=============
The point tracker is most useful to compute and show growth and displacement
fields on biological tissues. From a series of images of a biological sample
over time, the user can select material points over the various images, create
cells, and compute the growth rates for each cells over time.
Installation
------------
### From source
You can get the source either by cloning the repository or getting an archive
that you uncompress. The application can then be used in-place, or you can
install it with:
$ python setup.py install
### Using pip
From pip, you can simply use:
$ pip install point-tracker
Launching
---------
### When installed on the system
The setup script will create and install a ``point_tracker`` program on your
system, that you simply need to launch:
$ point_tracker
### From the source folder
From the source folder, you can use one of the tracking script:
$ python tracking.py
Under Linux, you can also use the shell script:
$ ./tracking.sh
Acknowledgements
----------------
If you are using this software for scientific purposes, please cite the
following paper:
> Kuchen, E. E.; Fox, S.; Barbier de Reuille, P.; Kennaway, R.; Bensmihen, S.;
> Avondo, J.; Calder, G. M.; Southam, P.; Robinson, S.; Bangham, A. & Coen, E.
> **Generation of leaf shape through early patterns of growth and tissue
> polarity**. *Science*. 2012, 335, 1092-1096
Bibtex reference:
@Article{Kuchen12,
Title = {Generation of leaf shape through early patterns of growth and tissue polarity.},
Author = {Kuchen, Erika E and Fox, Samantha and {Barbier de Reuille}, Pierre and Kennaway, Richard and Bensmihen, Sandra and Avondo, Jerome and Calder, Grant M and Southam, Paul and Robinson, Sarah and Bangham, Andrew and Coen, Enrico},
Journal = {Science},
Year = {2012},
Month = Mar,
Number = {6072},
Pages = {1092--1096},
Volume = {335},
Pii = {335/6072/1092},
Pmid = {22383846},
}
=============
The point tracker is most useful to compute and show growth and displacement
fields on biological tissues. From a series of images of a biological sample
over time, the user can select material points over the various images, create
cells, and compute the growth rates for each cells over time.
Installation
------------
### From source
You can get the source either by cloning the repository or getting an archive
that you uncompress. The application can then be used in-place, or you can
install it with:
$ python setup.py install
### Using pip
From pip, you can simply use:
$ pip install point-tracker
Launching
---------
### When installed on the system
The setup script will create and install a ``point_tracker`` program on your
system, that you simply need to launch:
$ point_tracker
### From the source folder
From the source folder, you can use one of the tracking script:
$ python tracking.py
Under Linux, you can also use the shell script:
$ ./tracking.sh
Acknowledgements
----------------
If you are using this software for scientific purposes, please cite the
following paper:
> Kuchen, E. E.; Fox, S.; Barbier de Reuille, P.; Kennaway, R.; Bensmihen, S.;
> Avondo, J.; Calder, G. M.; Southam, P.; Robinson, S.; Bangham, A. & Coen, E.
> **Generation of leaf shape through early patterns of growth and tissue
> polarity**. *Science*. 2012, 335, 1092-1096
Bibtex reference:
@Article{Kuchen12,
Title = {Generation of leaf shape through early patterns of growth and tissue polarity.},
Author = {Kuchen, Erika E and Fox, Samantha and {Barbier de Reuille}, Pierre and Kennaway, Richard and Bensmihen, Sandra and Avondo, Jerome and Calder, Grant M and Southam, Paul and Robinson, Sarah and Bangham, Andrew and Coen, Enrico},
Journal = {Science},
Year = {2012},
Month = Mar,
Number = {6072},
Pages = {1092--1096},
Volume = {335},
Pii = {335/6072/1092},
Pmid = {22383846},
}
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