BioBench - a workbench for biologists


National Botanic Garden of Belgium


This page centralizes the project information :

The camera

First results

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 (PDF)


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 :

On a list of images, must allow to :

[*]:working, [+]:in development, [~]:project

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.