Difference between revisions of "Software"

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(Windows, Mac, Linux)<br><br>
 
(Windows, Mac, Linux)<br><br>
 
Output from VolViewer has appeared in:<br>
 
Output from VolViewer has appeared in:<br>
[http://www.amazon.co.uk/Handbook-Plant-Science-Keith-Roberts/dp/0470057238/ref=sr_1_19?s=books&ie=UTF8&qid=1289321357&sr=1-19 Front cover: Handbook of Plant Science] | [http://www.plantcell.org/content/18/9.toc Front cover: The Plant Cell] | [http://www.rms.org.uk/Resources/Royal%20Microscopical%20Society/infocus/Edgar%20article.pdf  Royal Microscopical Society: Infocus Magazine] | [http://www.bioptonics.com/Home.htm Bundled with the Bioptonic 3001 scanner: Bioptonics Viewer] | [http://www.guardian.co.uk/science/gallery/2007/sep/04/fruitflybrain#/?picture=330675671&index=1 The Guardian newspaper: 3D Fruit fly] | [http://qt.nokia.com/qt-in-use/ambassadors/project?id=a0F20000006LZ2pEAG Qt Ambassador program] | [http://www.triffidnurseries.co.uk/special3.php Triffid Nurseries website]
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[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [http://www.amazon.co.uk/Handbook-Plant-Science-Keith-Roberts/dp/0470057238/ref=sr_1_19?s=books&ie=UTF8&qid=1289321357&sr=1-19 Front cover: Handbook of Plant Science] | [http://www.plantcell.org/content/18/9.toc Front cover: The Plant Cell] |  [http://www.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [http://www.rms.org.uk/Resources/Royal%20Microscopical%20Society/infocus/Edgar%20article.pdf  Royal Microscopical Society: Infocus Magazine] | [http://www.bioptonics.com/Home.htm Bundled with the Bioptonic 3001 scanner: Bioptonics Viewer] | [http://www.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [http://www.guardian.co.uk/science/gallery/2007/sep/04/fruitflybrain#/?picture=330675671&index=1 The Guardian newspaper: 3D Fruit fly] | [http://qt.nokia.com/qt-in-use/ambassadors/project?id=a0F20000006LZ2pEAG Qt Ambassador program] | [http://www.triffidnurseries.co.uk/special3.php Triffid Nurseries website]
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|width="50%"|  VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. VolViewer uses [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt] to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and  optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).
 
|width="50%"|  VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. VolViewer uses [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt] to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and  optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).

Revision as of 18:42, 17 December 2012

Current activity: a collaboration with the CoenLab with the aim of understanding how patterns of gene activity in biological organs influence the developing shape. The BanghamLab is focussed on the conceptual underpinning: concepts captured in computational growth models, experimental data visualisation and analysis.

Notes on documenting our software

Transferring Matlab files and zipping toolboxes and dependencies

Computational biology toolboxes

Quantitative understanding of growing shapes: GFtbox

For modelling the growth of shapes.

What? How? Where?

Tutorials: from the beginning

Examples: from publications

Download GFTbox from SourceForge
Download GFTbox project files:
Leaves Kuchen et al 2012
Principles and concepts Kennaway et al 2011
Snapdragon Green et al 2011, Cui et al 2010

Ready Reference Manual

(PC, Mac, Linux, uses Matlab
no Mathworks toolboxes needed
Matlab 30 day free trial and
student edition)

GFtbox is an implementation of the Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos (Kennaway et al 2011).

The GPT-framework was used to capture an understanding of (to model) the growing leaf (Kuchen et al 2012) and Snapdragon flower Green et al 2011. The Snapdragon model was validated by comparing the results with other mutant and transgenic flowers Cui et al 2010.

The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. (Kennaway et al 2011)

Viewing and measuring volume images: VolViewer

For viewing and measuring volume images on both normal and stereo screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images

What? How? Where?

Tutorials: from the beginning

Download

(Windows, Mac, Linux)

Output from VolViewer has appeared in:

Cell: Online Gallery | Front cover: Handbook of Plant Science | Front cover: The Plant Cell | American Scientist | Royal Microscopical Society: Infocus Magazine | Bundled with the Bioptonic 3001 scanner: Bioptonics Viewer | The Daily Mail | The Guardian newspaper: 3D Fruit fly | Qt Ambassador program | Triffid Nurseries website



VolViewer is used as a stand-alone app. or as a viewport for other systems, e.g. Matlab programs. VolViewer uses OpenGL and Qt to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment (OME).

Analysing shapes in 2D and 3D: AAMToolbox

For analysing populations of shapes and colours within the shapes using principal component analysis.

What? How? Where?

Tutorials: from the beginning

Download revised Nov2012


(PC, Mac, Linux, uses Matlab
no Mathworks toolboxes needed
Matlab 30 day free trial and
student edition)

The AAMToolbox enables the user analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading (Matthews et al. 2002version of pdf), we have used it extensively for analysing the shapes of leaves (Langlade et al 2005.,Bensmihen et al. 2010) and petals (Whibley et al 2006,Feng et al. 2010). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.

Analysing the shapes of clones: SectorAnalysisToolbox

For analysing the shapes of marked cell clones.

What? How? Where?

Tutorials: from the beginning

Download

(PC, Mac, Linux, uses Matlab
no Mathworks toolboxes needed
Matlab 30 day free trial and
student edition)

The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.

Open source systems to which we contribute

OMERO

For working with the OME image database.

See Details, Download
OMERO Workshop

(Windows, Mac, Linux)

Open Microscopy Environment Remote Objects (OMERO). for visualising, managing, and annotating scientific image data. See also our OMERO Workshop training course we ran in April 2011.

Tools and Utilities

BioformatsConverter

For converting microscope manufacturer proprietary file formats.

See Details

(Windows, Mac, Linux)

This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the Bioformats library.

In development

MTtbox

For modelling the behaviour of microtubules within a cell.

See Details

(Windows, Mac, Linux)

In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments.

The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.

Algorithms

Reaction-diffusion and morphogenesis

Tentacles morphogenesis.png

Illustration of morphogenesis inspired by Turing's paper.

Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip

1 A

A simple reaction-diffusion system develops a pattern of spots.


<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0004.flv|GPT_rd_rk_tentacles_20120417-0004_First.png</wikiflv>
Two simple growth rules translate the pattern into directed growth. The changing geometry that arises through growth causes the reaction-diffusion patterning to continue to change.


<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0001.flv|GPT_rd_rk_tentacles_20120417-0004.png</wikiflv>

Non-linear signal processing

Art