BioBench - a workbench for biologists
National Botanic Garden of Belgium
This page centralizes the project information :
- April 2007 : discovery of the hi-resolution (1.3 Mpix) webcam
- May 2007 :
- first success with Logitech's Quickcam for Notebook Pro 1.3 Mpix, at the resolution of 960x720
(UVC driver, Laurent Pinchart and luvcview, Michel Xhaard)
- definition of Taxbench GUI, written in Qt4-ruby
- new version of luvcview (20070512), allowing to take 1280x960 pictures
- September 2007 : Advance at the BioBench front (PDF)
- layout restructuration
- more working parts
- multiple measurement objects on the same image (counts, segments, length/width...)
- interface to the 'R' statistical package (start)
| First images taken at a lower resolution (960x720); for the microscope,
the optical axes are not yet well aligned : this is the first steps of a work in progres.
|Hires Webcam for macrophotos; 960x720|
|May, 14th : Michel Xhaard email me the new version of luvcview, supporting now to save pictures
with the highest resolution (1280x960) !
||Hires Webcam for microphotos; 960x720|
|First pictures taken at the highest resolution (1280x960), owing to the newest luvcview release
||the reference mid-gray grid background (white squares = 1 cm2), webcam objective heavily screwed off
||the same grid background (black squares = 1mm2), at the printer wax drop level (Tektronix 850) : the webcam
objective is fully unscrewed, then gently screwed for 1/4 turn
||a leaf of bryophyte (moss), seen with a microscope and the objective-less webcam
A 'good-enough' approach
As a rule, the research apparatus are very expensive : the camera provided with our Olympus research microscope
is not an exception : costing more than 6000 euro with its application program. Moreover, the program requires
a Microsoft platform.
It would be a pity to switch to Microsoft just to use a camera.
As the new webcams have a higher definition (1280x960 pixels), it makes now sense to use them for the day-to-day work.
The image taken with the cooled professional camera is surely less noisy, but I hope to cope with this problem when
needed with the averaging of a few snapshots.
Requirements to mount a camera on a microscope or a binocular
The camera must be lightweight and the objective MUST be removable. I choose the Logitech's Quickcam for
Notebook Pro 1.3 Mpix for its exceptional small size, and despite seemingly fixed, its easily removable objective.
|General view; the objective seems fixed
|one small screw is securing the two parts of the camera enclosure
|the enclosure opened : the objective is screwable, and will allow to make close-ups
(see the first examples) and to be easily removed for use on a microscope; see the thin screw in the background
REM: the special background is designed to provide a scale with color references, and a mid-gray average to help
the white balance of macrophotographies
|the objective is now unscrewed
|the CCD chip is now visible
|proof-of-concept : first try to position the CCD chip along the optical axis of the microscope :
the carboard piece
|and a cylindrical cardoard part (fastened with duct tape) to position the ensemble above
the vertical camera tube of the microscope
|or even in place of the regular eyepiece : ordinary microscopes do not have the vertical camera well,
and the especially lightweight quickcam allows to transform any microscope into a microphotography workplace
|| Very rough try !|
BioBench, the GUI
First working steps :
September 2007 : Advance at the BioBench front
The BIOLOGIST worbench (version 0.1.3 : 2007-05-11)
is designed to interface the images taken from a biologist's day to day work.
In fact it may be of more general usage, but I begin to solve my own problems first !
It will allow to :
- interface directly with the connected acquisition(s) device(s) [+]
- identify the sample (collector-collnum : 'BR:Empain.A-1789' ) and the magnification (CAM/BIN/MIC: mm/1000pixels) [~]
- label what it is(4 hex digit hierarchical code : say 4552='branch: leaf: apex: cells' ) [~]
- rename the image as name+code (fi. easy retrieval of all apical cells images, or any branch-related images...) [~]
On a list of images, must allow to :
[*]:working, [+]:in development, [~]:project
- browse the new pictures acquired from the camera/macro/microscope [*]
- zoom, crop, enhance the image [+]
- define, label and export ZOI (zone of interest) [+]
- insert an explicit scale (linear or as a grid) [*]
- make counts and measures [*]
- output statistics and interface them with R for subsequent analysis [+]
- bundle the acquired information, statistics and subsamples (ZOI) in a bag file 'a la OpenOffice', perhaps keeping the annotations and ZOI simply as locations/text and rectangle definition, to allow to build on-the-fly the derivated images -- keeping permanently only the untouched master image [~]
build true RDBS records owing to the embedded information [~]
- support scriptable default behaviour for repetitive tasks [~]
- can be distributed on a bootable CD
Alain EMPAIN -- 2007
In previous developments, I used perl and Qt3; I discovered Ruby last year and gave it a try with its Qt3 bindings.
Now, I decided to begin with Qt4-Ruby to develop my knowledge of this nice couple.