Download Investigating Plant Growth Using AVS Dr. R. P. Fletcher University of

November 8th 1999
UAUUG Birmingham
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Investigating Plant Growth
using AVS
Presentation to the
UK AVS and Uniras User Group Meeting
University of Birmingham
November 8th 1999
Dr. R. P. Fletcher
University of York
A report on work done by:
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Dr. S. M. Bougourd, University of York
Dr. C. L. Wenzel, University of York
… in collaboration with
Dr. J . Haseloff, MRC Laboratory of Plant
Science, Cambridge
• …and me
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Outline
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Which part of plant growth?
Which plant?
Why?
How?
How we use AVS
What we want to do (with AVS?)
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Which part of the plant?
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Above or below ground?
For us … below
This means the ROOTS
Specifically …
How do the root cells differentiate?
Which cells elongate and why?
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Which Plant?
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Aribidopsis thalinana
A member of the brassica family
Also known as:
Thale cress
or …
Mouse Eared cress
It’s a weed!
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Just so you know what it looks like
Whole Plant
Flowers
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… and there’s more ...
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Why use this weed?
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Small size and rapid life cycle
Prolific seed production
Simple genome
Many mutants and transformed populations
Perturb the behaviour of targeted cells
Monitor phenotypic expression
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The goal
“To understand the genetical and
cellular interactions that co-ordinate
the development of the root meristem”
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How we acquire the data
• Roots are visualised using Laser Scanning
Confocal Microscopy (LSCM)
• Also known as Confocal Scanning Laser
Microscopy (CSLM)
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Quick tutorial on CLSM
• A scanning laser beam is focussed onto a
fluorescent specimen
• Mixture of reflected and emitted light is
captured by a photo-multiplier via beam
splitter
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Tutorial continued
• Arranged so only the emitted light enters
the photo-multiplier
• A confocal aperture (pin-hole) placed in
front of the photo-multiplier
• The effect is to only allow emitted light
from the “in focus” area to pass into the
photo-multiplier
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Principles
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Typical System
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The real thing
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Interesting problem?
• Its all very well staining specimens so that
they fluoresce, but ...
• We need to see whole root tip, not just
sections and ...
• We need same level of staining throughout,
but ...
• Normal stains kill the cells and are bleached
by the laser scanning process
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The Solution!
• Everybody’s buzzword these days
• Genetic Modification!
• The idea is to get the plant to manufacture
its own fluorescent stain
• So, we will borrow a gene from somewhere
else in the natural world
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Obtaining the Gene
• Plenty of naturally fluorescent plants and
animals out there
• The oceans are full of them
• The jellyfish, Aequorea victoria, from the
Pacific Ocean has been used.
• They produce the protein, Green
Fluorescent Protein (GFP).
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Wibbly Wobbly Jellyfish
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Pretty, Pretty
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… and they can swim
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Getting the Gene into the Plant
• A quick tutorial about genetic modification
• … gene extracted ... put in vector, a soil
bacterium … isolate “infected cells” and
regenerate whole plants.
• Can even link “instructions” to the GFP
gene to make the plant only produce the
fluorescent protein in certain parts of the
plant
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A Single Image
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An Image Stack
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Getting this Stack into AVS
• The old nutshell!
• First, find out the format of the Bio-Rad
PIC files.
• Hunt round for some “v” … IAC maybe?
• Got some code, but was developed for
ALPHA
• Had “endian” problems
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Fix the code and develop
Visualisation Modules
• Fix the “v” code to read the correct “endianness” of the data
• Amount of data can be a problem
• 512 * 768 * stack size (loadsa data!)
• Hope the decimation modules in Version 5
will help here
• Even running on 350Mhz PC or SGI 02,
both with 128 Mb of memory, AVS is slow
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Network for preliminary viewing
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Using AVS to view along a
different axis
tip
Single frame
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Back a bit
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Movie view along the axis
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What are we actually seeing?
• GFP fluorescing in the cell walls
• The higher the intensity the more GFP
• Would be better to invert the images
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Inverted Image Stack
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Non-invasive non-lethal
• The use of the GFP means we can study the
plant root growth “in vivo”
• The aim is to understand the fate of the
different root tip cells
• Need to find a way to “tag” cells from one
image stack to another
• Time dimension
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Cell fate?
Divide
Root tip cell
Differentiate
Some just grow
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Some elongate and grow
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Need to see 3D view
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3D reconstruction from “cloud of points”
Need to “cut away”
Need to “identify” cells
Need to track “fate”
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Preliminary 3D Investigation
Orthoslices
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Animate the orthoslices
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Complex Network
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Add in some “real” 3D
Volume
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Another View
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Animated volume cutaway
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So just how useful is AVS?
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Using AVS can really help to see the data
Reconstructing different orthogonal views
Volume visualisation will help
Data volume is a problem on “small”
systems
• Decimation routines will be welcome
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Future Work
• Need to work out how to mark cell volumes
in order to track specific cells
• Create new fields from marked data
• Visualise these “new” fields with time “n”
images
• Difference frames may help from time “n”
to time “N+1”
• Big data processing effort here needed
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THAT’S
ALL
FOLKS
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