Latest
Doube M, Firth EC & Boyde A Variations in articular calcified cartilage by site and exercise in the 18-month-old equine distal metacarpal condyle Osteoarthritis Cartilage 15:1283-1292 (2007) PMID: 17517523
Drishti!
A new animation using Drishti is here (4.4 MB wmv).
 Added 27-04-2007 | Drishti is an open source volume rendering program written by Ajay Limaye and made available for download by the Australian National University. I've been using it to create animated renderings of microCT scans of a fracture predilection site in equine third metacarpal bones. I found that my old nVidia graphics card wasn't supported so bought a GeForce 7600 GS with 512 MB video RAM, which works pretty well. Sample animated renderings are here: Thanks to Graham Davis for introducing me to the program and for doing the microCT! |
Volume Slicer
 Added 12-03-2007 | Volume Slicer is an ImageJ macro for animating sequential volume renderings of 3D image stacks. It asks the user to enter rotation and slice variables in a GUI dialog box, then sends the variables to Kai Uwe Barthel's Volume Viewer 3D rendering plugin. |
Umis Array
 Added 30-12-2006 | Umis Array is an ImageJ macro for the correlated measurement of nanoindentation modulus and tissue mineralisation density, however it could be modified to map any set of coordinates to an image if they are provided as a comma-separated file with marker points at all 4 corners of a rectangular array area. |
SCANNING Paper
Doube M, Firth EC & Boyde A Registration of Confocal Scanning Laser Microscopy and Quantitative Backscattered Electron Images for the Temporospatial Quantification of Mineralization Density in 18-Month Old Thoroughbred Racehorse Articular Calcified Cartilage SCANNING 27(5) p219-226 (2005) PMID: 16268174
NZVJ Paper
Firth EC, Rogers CW, Doube M & Jopson NB Musculoskeletal responses of 2-year-old Thoroughbred horses to early training. 6. Bone parameters in the third metacarpal and third metatarsal bones New Zealand Veterinary Journal 53(2) p101-112 (2005) PMID: 15846394
Physis animation
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Confocal depth series of a mouse physis (growth plate) rendered in ImageJ and animated with Avidemux. Green is calcein labelling of mineralising bone and cartilage, blue is reflection from the physeal cartilage and orange is tissue autofluorescence. Frame width 612 microns. Made on a Fedora Core 3 Linux box. Open in your media player and set it to loop continuously. Thanks to Duncan Bassett of Imperial College for the use of the specimen (24/05/2005) |
SCANNING cover
Registered (overlapped) CSLM and BSE images Selected for the cover of the Scanning 2005 Proceedings Issue (01/03/2005)
Perl script!
My First Perl Script - in fact my first ever working, useful program. Takes the profile data from ImageJ (below), calculates intervals based on labelling times then squirts it all out in tab-separated columns (20/02/2005)
#!/usr/bin/perl
#kittyflip.plx
use warnings;
use strict;
my $fname;
my $line;
my @pre_profile;
my $element;
my $interval;
my $count;
my @profile;
my $density;
my $pixel_time;
my $i;
my @line;
my $row;
my $col;
my $array;
my @array;
my @namechars;
my $out;
print "Please ensure that the input filename takes\nthe general form,
hhlsppxxxxx, where\nhh is the horse id, l is the leg, s is the slice
and pp is the site.\nData will be added at the bottom of an existing
output file, otherwise a new file will be created.\nPlease enter an
output file name\n: ";
$out = <STDIN>;
open FH, ">> $out" or die $!;
print "How many days between labels?: ";
$interval = <STDIN>;
foreach $fname(@ARGV) {
open(FILE, $fname) || die("Could not open $fname\n");
@namechars = split(//,$fname);
$row=0;
while (<FILE>) {
s/[\n\r]+$//;
s/(^ +| +$)//g;
@line=split(/\t/,$_);
for ($col=0;$col <= $#line;$col++) {
$array[$col][$row]=$line[$col];
}
$row++;
}
for ($row=1;$row <= $#array;$row++) {
$line='';
for ($col=0;$col <= $#{$array[$row]};$col++) {
$line.="\t$array[$row][$col]";
}
$line =~ s/^\t//;
chomp $line;
@pre_profile=split(/\t/,$line);
shift @pre_profile;
@profile = ();
for $element(@pre_profile) {
unless($element == 0) {
push @profile, $element;
}
}
$count = @profile;
$pixel_time =
$interval/$count;
$i = $pixel_time;
for $density(@profile) {
print FH
$namechars[0],$namechars[1],"\t", $namechars[2], "\t",
$namechars[3], "\t", $namechars[4],$namechars[5], "\t",
$i,"\t", $density, "\n";
$i = $i + $pixel_time;
}
}
close(FILE);
}
print "Data written to ", $out;
Correlated qBSE and confocal measures
Using Sync Windows in ImageJ to measure mineralisation density (qBSE image, right) using calcein labels as temporospatial reference points (CSLM image, left). Going for DJD/OOS in my middle finger to match that in my first finger. The things we do for thousands of data points...(08/02/2005)
Articular calcified cartilage animation
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DivX animation of equine articular calcified cartilage and osteons, Intra-vitally labelled with tetracycline and imaged with CSLM Leica SP2 scanhead; 40x objective; 488nm excitation; Reflection (blue), FITC (green) and longpass (red) filters Image stack is 375µm x 375µm x 46µm Image processing performed with ImageJ (16/12/2004) |
Step into the lab...
The SEM room. 'Nuf sed (29-11-2004)
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This file last modified 2006hrs 08 November 2007 © Michael Doube 2004-2008 :: Designed to be interoperable and standards-compliant. Looks best with Mozilla Firefox