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Gel Documentation System

BioDocAnalyze (BDA) digital


Order Numbers
034-000, 034-050, 034-302,
034-312, 034-303, 034-313

Instructions for Installation


and
Image Acquisition
Software Version 2.66.3.0
9-990-017/english
Version 04_11

Please read the operating instructions carefully


before using the system!

Biometra GmbH
D-37079 Gttingen
Rudolf-Wissell-Strae 30
D-37079 Gttingen
Tel.:
+49 551 50686-0
Fax:
+49 551 50686-66
e-mail: Info@biometra.com
internet: http://www.biometra.de

Service
Rudolf-Wissell-Str. 14-16
D-37079 Gttingen
Tel.:
+49 551 50881-10/12
Fax:
+49 551 50881-11
Service@biometra.com

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means without the prior written permission of Biometra GmbH nor be otherwise circulated electonically or in print.
In no event Biometra GmbH shall be liable for indirect, incidential or consequential damages
resulting from the use of the information supplied by this manual. This manual was written
with due care and Biometra GmbH shall not be liable for any fault or omission.
September 2011.
Tradenames of software or hardware cited herein, esp. those of the Microsoft Corp., are registered, patented or protected by other legal means.

BDAdigital Manual, Vers. 04_11

Contents

Contents
1

INSTALLATION OF BDADIGITAL...................................................................................................4
1.1
COMPONENTS ..............................................................................................................................4
1.2
ASSEMBLY ...................................................................................................................................4
1.2.1
Personal computer and monitor..........................................................................................4
1.2.2
Copy protection (Dongle, Hardlock)....................................................................................4
1.2.3
Set up of single lens reflex camera.....................................................................................5
1.2.4
Bandpass Filter ...................................................................................................................7
1.2.5
Filter wheel labels ...............................................................................................................8
1.2.6
Mounting the camera at BDA Hood ....................................................................................8
1.2.7
Mounting the camera at BDA Box 1/2/3 .......................................................................... 10
1.2.8
Darkhood, transilluminator and converter plate............................................................... 11
1.2.9
Thermal printer................................................................................................................. 11
1.3
INSTALLATION OF THE SOFTWARE .............................................................................................. 12
1.3.1
Overview .......................................................................................................................... 12
1.3.2
Installation of the Camera Canon EOS 1100D (optional)................................................ 13
1.3.3
Installation of the BioDocAnalyze Program ..................................................................... 14
1.3.4
Installation of Thermal Printer Mitsubishi P95DE ............................................................ 15

START OF THE PROGRAM ......................................................................................................... 15


2.1

CHOICE OF MAIN WINDOWS ........................................................................................................ 16

BDADIGITAL IMAGE CAPTURE WITH SINGLE LENS REFLEX CAMERA, E.G. EOS 1100D. 17
3.1
THE IMAGE CAPTURE................................................................................................................. 18
3.2
FUNCTIONS AND CAPTURE PARAMETERS .................................................................................... 19
3.2.1
Profiles with Capture Parameters .................................................................................... 19
3.2.2
The Card Settings ......................................................................................................... 20
3.2.3
Camera Settings for Typical Gels .................................................................................... 21
3.2.4
Further Functions for Image Capture............................................................................... 22
3.2.5
Take photo and display settings ...................................................................................... 23
3.2.6
Basic functions................................................................................................................. 24
3.2.7
The Gel Picture Window .................................................................................................. 24

BDADIGITAL IMAGE CAPTURE WITH DIG. COMPACT CAMERA, E.G. POWERSHOT G10 . 25
4.1
THE IMAGE CAPTURE................................................................................................................. 26
4.2
FUNCTIONS AND CAPTURE PARAMETERS .................................................................................... 27
4.2.1
Profiles with Capture Parameters .................................................................................... 27
4.2.2
The Card Settings ......................................................................................................... 27
4.2.3
The Card Advanced ...................................................................................................... 29
4.2.4
Camera Settings for Typical Gels .................................................................................... 30
4.2.5
Further Functions for Image Capture............................................................................... 31
4.2.6
Take photo and display settings ...................................................................................... 32
4.2.7
Basic functions................................................................................................................. 33
4.2.8
The Gel Picture Window .................................................................................................. 33

SERVICE........................................................................................................................................ 34

EQUIPMENT DECONTAMINATION CERTIFICATE .................................................................... 35

DISPOSAL ..................................................................................................................................... 37

BDAdigital Manual, Vers. 04_11

Installation

1 Installation of BDAdigital
concerning
034-000 BDAdigital core set
034-050 BDAdigital compact
034-302, 034-312 BDAdigital System 20
034-303, 034-313 BDAdigital System 30

1.1 Components
The system comes with:
-

BDA software (CD-ROM) and manual


Dongle (copy protection key, hardlock)
Digital camera inclusive power supply
Bandpass filter BP595 for EtBr stained gels

Additionally with BDAdigital compact:


-

Darkhood BDA Hood incl. anti-theft camera mounting

Additionally with BDAdigital System 20 and BDAdigital System 30:


-

darkhood BDA Box 2 incl. anti-theft camera mounting


Transilluminator UVstar 20 resp. UVstar 30
UV converter plate
Thermal printer incl. USB cable
TFT monitor
Personal computer, installed

1.2 Assembly
1.2.1 Personal computer and monitor
Attach the cable of the monitor to the VGA port of the graphic card of the PC.
Connect also mouse and keyboard to the computer. Connect monitor and PC via cable with
the appropriate power supply system.
Compatible operational systems: Windows XP and Windows 7

1.2.2 Copy protection (Dongle, Hardlock)


The BioDocAnalyze software is protected by a copy protection key (dongle, hardlock).
Note: The dongle is the software licence.
The dongle is supplied as key for the USB port of the computer.
This dongle is plugged to the USB port of the computer.
After installation the dongle is automatically detected and flashes in
red.

BDAdigital Manual, Vers. 04_11

Installation
1.2.3 Set up of single lens reflex camera
The following instructions focus to the basic installation steps.
Please also refer to the camera instruction manual supplied on the CD-ROM with the Canon
camera.

1.2.3.1 Attaching the lens to the camera


Remove the caps.
Remove the rear lens cap and the
body cap by turning them as shown
by the arrows.

Attach the lens.


Align the lens red or white index with
the cameras index matching the
same color. Turn the lens as shown
by the arrow until it snaps in place.

On the lens, set the focus mode


switch to <AF> (autofocus).
If it is set to <MF> (manual focus),
autofocus will not operate.

Remove the front lens cap.

Note:
Minimizing Dust

When changing lenses, do it in a place with minimal dust.


When storing the camera without a lens attached, be sure to attach the body cap to the
camera.
Remove dust on the body cap before attaching it.

BDAdigital Manual, Vers. 04_11

Installation
1.2.3.2 Attaching the power supply to the camera
Connect the power cord.
Connect the power cord as shown in the figure.

Connect the DC Coupler.


Connect the DC cords plug to the DC Coupler.

Insert the DC Coupler.


Open the cameras battery compartment cover sliding
the lever. Insert the DC Coupler until it locks in place.

Push in the DC cord.


Open the DC cord groove cover and install the cord as
shown.

Close the cameras battery compartment cover.

BDAdigital Manual, Vers. 04_11

Installation
1.2.3.3 Attaching the USB to the camera
Note:
In case that you also want to use the Canon software included in the camera delivery for
other applications independend from BDAdigital please install the Canon software before you
connect the camera to the computer!
The Canon software is not required for running the camera under BDAdigital.

Open the terminal cover and connect the USB cable


to the USB.
Connect the other side of the USB cable to the USB
port of the computer.
Note:
To avoid any hardware detection problems it is highly
recommended to connect a USB device always to the
same terminal of the computer where it was initially
installed.

1.2.4 Bandpass Filter


Standard delivery is a red bandpass filter with transmission maximum of 590 nm for the typically used fluorescent stain ethidium bromide. For other stains please request for applicable
optional filters.
1.2.4.1 With small darkhood BDA Hood of BDAdigital compact, BDA Box 1 or a stand:
Please screw the bandpass filter directly to the camera zoom lens.
For image acquisition of coloured samples, e.g. silver or Coomassie Blue stained gels, illuminated with white light no bandpass filter is needed.
1.2.4.2 With Darkhood BDA Box 2 or BDA Box 3:
Please insert the bandpass filter into the filter wheel: Open the darkhood sliding door and
open the UV protection shield up to a horizontal position. Slowly pull out the filter wheel with
the knob inside the darkhood, below the filter wheel. The filter wheel is slided out and the
filter can be inserted into the wheel. Please choose the wheel position which is opposite to
the corresponding filter label (see 1.2.5).
Note:
Filters with slightly higher filter holder shall be inserted in borehole Nr. 3 of the filter
wheel. Then Nr. 1 is seen at filter wheel front.

BDAdigital Manual, Vers. 04_11

Installation
1.2.5 Filter wheel labels
Delivery of a BDA Box includes several small filter wheel labels.
These labels can be applied to darkhoods with filter wheel (BDA Box 2, BDA Box 3) at the
front panel of the filter wheel. Please note that the visible front position number corresponds
to the opposite filter wheel position. The standard delivery of BDA systems includes the red
590 nm/ethidium bromide filter.
The green 520 nm/SYBR Green filter and also the yellow wide pass filter with transmission
range of 490 nm up to 690 nm can be bought as optional components.

1.2.6 Mounting the camera at BDA Hood


in BDAdigital compact sets

1. Mounting of camera

Camera incl. zoom


lens and screwed
bandpass filter

Light trap

Hexagon socket
for screwing the camera
to the bracket.
Camera bracket.
By slight release
of the two knurled
head screws the
bracket can be
moved forward
and backward as
well as left and
right for straight
alignment of the
camera (please
check by manual
zooming that no
resistance or
noise is noted!).

BDAdigital Manual, Vers. 04_11

Installation
2. Covering of lens release
Special screw

Cover for lens release


button.
Please push the pin
through the left slot and
slide the cover up towards
the camera.

3. Security bracket

Special
screw driver

Special
screw driver

Special screws
Security bracket

Mounted cover for


lens release button

BDAdigital Manual, Vers. 04_11

10

Installation

1.2.7 Mounting the camera at BDA Box 1/2/3

1. Mounting of camera
Camera incl.
zoom lens
(with BDA Box 1:
with screwed
bandpass filter)

Hexagon socket
for screwing the camera
to the bracket.
Camera bracket.
By slight release
of the two knurled
head screws the
bracket can be
moved forward
and backward as
well as left and
right for straight
alignment of the
camera (please
check by manual
zooming that no
resistance or
noise is noted!).

Light traps

2. Covering of lens release

Cover for lens release


button.
Please push the pin
through the left slot and
slide the cover up towards
the camera.

Special screw
Special
screw driver

BDAdigital Manual, Vers. 04_11

11

Installation
3. Security bracket
Special
screw driver
Security bracket

Special screws

Mounted cover for


lens release button

1.2.8 Darkhood, transilluminator and converter plate


Please refer to the separate operating instructions of the darkhood and the transilluminator.
The converter plate for application on top of the UV transilluminator for documentation of
samples with visible colour stains is delivered ready to use.

1.2.9 Thermal printer


!

To avoid any Windows problems with the USB ports it is recommended to connect USB devices to the same USB port as used for installation of the devices.

Connect the thermal printer Mitsubishi via USB cable with the PC. Connect the printer with
the power supply system and put a roll of paper into the printer.
Windows automatically recognizes the printer which is connected via USB cable as a new
instrument. Therefore the printer should only be switched on just before it shall be installed.
To avoid installation errors we recommend to install the thermal printer as last component of
the system.

BDAdigital Manual, Vers. 04_11

12

Installation

1.3 Installation of the Software


BDAdigital software with software version no. 2.66.3.0 and higher is compatible with
operational systems Windows XP and Windows 7.
The installation is only necessary in case you bought the sets 034-000 and 034-050
without a computer from Biometra. If BioDocAnalyze comes with a Biometra computer, the software is completely installed and the system is ready to use after unpacking and installing the cables.
PC minimum requirements: Personal computer with Windows XP or Windows 7/32 bit, processor dual core 1.6 GHz or similar, graphic card 1280 x 1024, 1 GB RAM, 3 USB2.0 ports,
CD-ROM drive.
For installation it is necessary to work with system administrator rights.
Software installation: This will take, depending on the computer and installation experience,
between 15 and 45 minutes. In case of problems during or after installation, please contact
the Biometra BioDocAnalyze customers service, phone +49(0)551-5068612, fax +49(0)5515088111, e-mail H.Becker@analytik-jena.de.

1.3.1 Overview
!

For installation procedure please refer to following chapters with detailed information.
completed

1.3.1.1 Installation of camera (s. 1.3.2).......................................................................F


Installation of digital camera driver and image editing and processing programs from Canon
CD-ROM (optional, not required for BDAdigital application)
Afterwards connect camera to PC.
1.3.1.2 Installation of BDA software incl. dongle (s. 1.3.3).......................................F
from BDA CD-ROM
1.3.1.3 Installation of thermal printer (s. 1.3.4) ..........................................................F
from BDA CD-ROM

BDAdigital Manual, Vers. 04_11

13

Installation
1.3.2 Installation of the Camera Canon EOS 1100D (optional)
!

The camera driver from the Canon Digital Camera Solution CD must be installed
before connecting the camera to the PC!

1.3.2.1 Installation of the Canon programs


1. Click [Easy Installation] to start installation.
2. Follow the windows displayed for the rest of the installation procedure.
3. When installation ends, the window with request for restart appears.
4. Click [Restart].

1.3.2.2 Basic camera settings


The camera is not yet connected to the PC.
1. To have correct dates on your pictures, the time and date in the cameras menue, card
settings, must be set.
2. Connect the camera with mains adapter with the power supply system.
3. In control panel, energy options the standby mode of the computer and the switch off
of the harddisk should be set to never as after reactivation the connection to the camera
may be lost. Switching off the computer monitor after some minutes of inactivity or the
screen saver will not disturb the camera function.

Afterwards connect the camera to the computer by its USB cable.


!
To avoid any Windows problems with the USB ports it is recommended to connect USB devices to the same USB port as used for installation of the devices.

Turning on the power


<ON> The camera turns on.
<OFF> The camera turns off. Set to this position when
not using the camera.

When the camera is connected to the computer the camera will automatically switch to the
PC mode. The computer mostly will show a short note that the camera is detected. In case
that a window of Canon or Windows software is opened asking for the next action with the
camera please close this request.

BDAdigital Manual, Vers. 04_11

14

Installation
Setting the Shooting Mode
Choose the mode Manual Exposure to be free to set both the shutter speed and the aperture manually. This mode is recommended for use with BDAdigital.
Set the Mode Dial to <M>.

1.3.3 Installation of the BioDocAnalyze Program


incl. the driver for the copy protection key (hardlock, dongle)
1. Insert the BioDocAnalyze installation CD into the PC drive. A window Automatic replay is opened. Choose Open directory for display of files or close the window and proceed with 2.
2. Start my computer or the Windows Explorer and choose the CD-ROM drive.
3. Start installation with double-click on the file BDAdigital_setup.bat in the main directory.
Now the drivers for the dongle and the BioDocAnalyze software are installed.
4. Confirm the request for completing the installation.
Note:
Starting the BDAdigital image acquisition window for the first time you are asked to
type in a 4-digit activation code to get free access to this software part. You will find
the requested code labeled to the copy protection key (see also section 3).

********************************************************************

It is also possible to install the BioDocAnalyze software and the drivers of the dongle separately:
BioDocAnalyze
software

Start the file BioDocAnalyze_setup.exe in the directory


BDA\Release\Single of the BioDocAnalyze CD and confirm all
requests.

Dongle

Start the file hdd32.exe in the directory HASP4_driver_setup


and confirm all requests.

********************************************************************

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15

Installation
BioDocAnalyze Software Update
When the BioDocAnalyze software shall be installed to an existing system as software
update only the BioDocAnalyze software has to be installed newly.
A new installation of other drivers and programs is not necessary.
Installation:
1. Please uninstall the existing BioDocAnalyze software version
by Start, control panel, Software, BioDocAnalyze with thedelete button or alternatively
by Start, All programs, Biometra, BioDocAnalyze, Uninstall BioDocAnalyze.
2. Now please install the BioDocAnalyze software from CD by double-click on the file
BioDocAnalyze_setup.exe in the directory BDA\Release\Single of the
BioDocAnalyze CD.
3. Confirm all requests.

Restart your computer. Switch on the thermal printer before so you will be asked for the
printer driver installation automatically.

1.3.4 Installation of Thermal Printer Mitsubishi P95DE


The default settings for printing in the configuration file biom1.ini of the BioDocAnalyze program are optimized for the thermal printer Mitsubishi P95DE with thermal paper KP65HM or
KP95HG-CE and thermal printer Mitsubishi P93DW with thermal paper KP65HM or
KP91HG-CE. In case another printer or another paper are used the printouts can be too
dark. Then an individual adaptation of setting values (printcontrast, printbrightness, printgamma) in the biom1.ini is recommended.
The printer drivers are on the BioDocAnalyze CD-ROM in the directory MitsubishiP9xx.
Windows XP:
The printer installation at the USB port runs widely automatically. Please confirm the different
requests as recommended from the system as standard installation.
Windows 7:
The Mitsubishi printer P95DE is not automatically installed under Windows 7.
Open Start/Control panel/System and security/System/Device manager. You will find Mitsubishi P95D with question mark under Other devices.
Please double-click on Mitsubishi P95D, select Driver and afterwards Refresh driver.
Browse to the BDA-CDROM in the computer CD/DVD drive for printer drivers. Now the
printer will be installed automatically.
The driver software was installed successfully is displayed. Now the printer is displayed as
standard printer unter Printer and fax machine.
Paper save mode
A possibility to use the thermal paper more efficiently is to activate the paper save mode in
the printer settings:
Choose Start, settings, printer & fax and open the dialog box of the thermal printer. Choose
card settings and set the paper save mode to on.
BDAdigital Manual, Vers. 04_11

16

Start of Program

2 Start of the Program


The program is started from the desktop by a LEFT MOUSE BUTTON DOUBLECLICK on to the
icon "BioDocAnalyze" or alternatively the command sequence "Start, Programs, Biometra,
BioDocAnalyze".
The BioDocAnalyze-Logo is opened and after several seconds displaced by the full frame
window "BioDocAnalyze" with a menu bar and a function bar.

2.1 Choice of main windows


The desired function is activated by click on the
icon in the function bar.

You have the choice between:

Image capture with digital CCD camera (BDA live)

Image capture with CCD video camera (BDAvideo)

Image capture with digital single reflex camera (DSLR BDAdigital)

Image capture with digital compact camera (BDAdigital)

Gel analysis.
This manual only refers to the image capture with the digital camera.
Gel analysis is described in the separate manual BioDocAnalyze.

BDAdigital Manual, Vers. 04_11

17

Image Capture DSLR

3 BDAdigital Image Capture


with Single Lens Reflex Camera, e.g.
EOS 1100D

The BDAdigital image capture software is started with a LEFT MOUSE BUTTON CLICK on the icon DSLR BDAdigital.

When starting the BDAdigital capture software


for the first time after installation you will be
asked for a 4-digit software code to activate
the capture screen.
The code comes along with the dongle.

The window Capture digital camera is opened and shows the detected camera in line
Camera.

Fig. 3-1

Window Capture digital camera

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18

Image Capture DSLR


Camera
In case that in line Camera only Model is shown the camera is not correctly installed or
not switched on. Please check and correct. Close the BDAdigital window and reopen again.
Profile
When the capture window is opened it starts with the camera settings of the last opened profile.
Shooting Mode
When the mode dial of the camera was correctly set to <M> (see chapter 1.3.2.2) the line
shooting mode will accordingly display M for manual mode.

3.1 The Image Capture


These are the typical steps for image capture:

1. Turn on the live preview:

2. Place the electrophoresis gel on the transilluminator.


3. Turn on the light source of the darkhood.
4. Straighten the gel with the help of the live preview in the transilluminator center.
5. Choose the desired zoom area: Turn the zoom ring on the
lens with your fingers.

6. Choose the appropriate settings profile:

7. Take a photo:
The select box AF is selected as default. As long as it is activated the camera will be
automatically focussing before taking the picture.
Note: The focus mode switch of the lens must be set to AF.
If it is set to MF (manual focus) autofocus will not
operate.

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Image Capture DSLR


8. If necessary optimize the exposure
time Tv and the lens aperture Av in
window Settings. Then take another
photo.
Note: These parameters can only be set in program mode M (manual).
Please consider: During image acquisition the live preview meantime is turned off as
the camera is not providing preview data at the same time. After finishing the image
acquisition the live preview is automatically shown again.

Please dont start any further functions of the BDAdigital software while the camera is
taking the image which may take some seconds.

9. Save and print the image:


For details please see section 3.2.

3.2 Functions and Capture Parameters


The window Capture digital camera is widely self-explaining and very similar to general
known parameters in photography. In spite of that the individual functions are explained in
the following.

3.2.1 Profiles with Capture Parameters


Profile

This includes some profiles with working parameters for the image acquisition of
certain gel types.
A mouse click on the profile will set the parameters in the camera. The corresponding parameters are shown in the cards Settings and Advanced. It is essential that
the Shooting Mode is manual otherwise the settings shown in the card Settings
will not really be the used parameters.
It is also possible to enter names for individual settings. After typing in the new
name and setting the parameters the new profile has to be saved .
Switch off of the live image will accelerate the change of profiles.

Save

This saves user-defined profiles under the active profile name.


Before saving you should check whether already a profile with the same name exists because it would be overwritten.

Clear

This deletes the active profile. The Biometra saved profiles can not be deleted.

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Image Capture DSLR


3.2.2 The Card Settings

Shooting Mode For display of capture mode (set at the camera). Recommended mode is
M (manual).
-

Exposure time and lens aperture can be set in lines Av and Tv. Even
for the use of profile parameters the mode should be M.

The camera sets the capture parameters exposure time Tv and lens
aperture Av automatically.
When the photo is taken the automatically used parameters are displayed
on card Shot Conditions.

Tv

The camera automatically chooses the optimal lens aperture Av in


relation to the manually set exposure time. After the picture is taken the
automatically used aperture is displayed in the card Shot Conditions.

Av

The camera automatically chooses the optimal exposure time Tv in


relation to the manually set lens aperture. After the picture is taken the
automatically used exposure time is displayed in the card Shot Conditions.

Lens aperture,
Av

For setting the lens aperture. A small aperture number stands for a wide
open lens, a high aperture number for a more closed lens. The depth of
focus increases with rising aperture number (= smaller lens aperture). Agarose gels, especially thicker gels, should be photographed with high aperture number (= small aperture). Otherwise photos may not be focussed.
The largest aperture (= small number) available depends on the zoom factor set. With zoom 55 mm the largest aperture is 5.65, with zoom 35 aperture 4 and with zoom 18 the largest possible aperture to be set is 3.5.

Exposure time, For setting the exposure time. The time is to be set in dependence of
sample/illumination and lens aperture. For smaller apertures (= high aperTv
ture number, e.g. 8) exposure times of up to 8 seconds can be necessary
for a photo of fluorescent gels.
Resolution

For choice of image resolution in pixels. The higher the resolution the
bigger the file size.
High resolutions will cause longer data transfer times from camera to PC
on computers with slow processors and memory below 512 MB RAM. For
an efficient operating it is recommended to use a computer with at least 1
GB RAM and a 2.8 GHz processor.

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Image Capture DSLR


EOS 1100D
Large + Fine
Medium + Fine
Small + Fine
Small S2

Resolution (pixels)

Compression

Approx. 12.2 MP
Approx. 6.3 MP
Approx. 3.4 MP
Approx. 2.5 MP

Fine
Fine
Fine
Fine

For setting of the sensitivity.

ISO

In most cases it is advised to use ISO 100. It provides sufficient sensitivity


by lowest background noise. Only for the acquisition of very faint signals at
high zoom factors it can be necessary to raise the sensitivity to higher ISO
scores.
Exposure
Compensation

For setting an exposure correction. A fine-tuning of the optimal exposure


can be done in small steps. This function is not available in shooting mode
M because lens aperture and exposure time are specifically set in the
manual mode.

3.2.3 Camera Settings for Typical Gels


The software provides camera settings for two typical gel types in Profiles. Starting with
these settings it is very easy and fast to optimize the camera settings for individual gels.
Gel type

EtBr Stained Agarose Gel Coloured Polyacrylamide


Gel
on UV table

on UV table with yellow


converter plate, without UV
filter on camera lens,
e.g. silver or Coomassie
Blue stained polyacrylamide gel

Profile DNA/EtBr

Profile Converter

Shooting Mode

Lens aperture Av

5.6

5.6

Exposure time Tv

8s

1/50 s

ISO

100

100

Resolution

Medium + Fine

Medium + Fine

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Image Capture DSLR


3.2.4 Further Functions for Image Capture

Live view
on/off

For turning on/off the live preview in window Live Preview.


Due to the high iteration frequency of the picture and for
this reason short exposure times it is possible that the live
preview will not be as bright and focussed as the real gel
picture.
Note: For camera protection reasons the live preview is
turned off after some minutes without any operation. It can
be turned on again with the button Live View on.

Focus bar and


Autofocus

Button Autofocus triggers the autofocus. As long as the selection box


AF beside button Take Picture is selected it is not necessary to release
Autofocus additionally before taking the image.

The arrow buttons are for manual focussing. For an easy optical control the magnification buttons beside the Live Preview can be used, see
below.
Magnification
buttons

For easy control of image sharpness during manual focussing (see above) an area of the preview image can be
enlarged by factor 5 resp. 10. Fit resets the magnification.

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Image Capture DSLR


3.2.5 Take photo and display settings

Take picture

This button triggers taking the image. The picture is transferred from the
camera to the computer and it is displayed on card Image.

AF

The select box AF is selected as default. As long as it is activated the


camera will be automatically focussing before taking the picture.

Rotate 180

For rotating the picture 180, for example when the gel is positioned the
opposite way round on the illumination table or when the camera is fixed
on the darkhood or stand with the camera control panel ahead.

Invert

For inverting of the gel picture. The use of this function is only senseful
with black&white pictures.

Show Grid

A grid can be displayed on top of the photo. This can be used as control
whether the gel is positioned in straight form. This is important for an accurate detection of lanes in a subsequent gel analysis.

Black & White


Mode

Activation of this function results in a change of the colour picture to a


grey-scale picture.

Saturation

Activation of this function sets areas of the photo to blue or red colour if
the signal reaches saturation. The photo display automatically switches to
the black&white mode.
The pixels of the area to be quantitatively analyzed later must not be
saturated, neither true white or true black. That means that the area of
interest must not be in blue or red colour. This can be achieved by shorter
exposure times or with smaller lens apertures (= larger lens aperture number).
When using longer exposure times it is possible that the live preview is
darker than the photo. This will cause differences in the saturation display
of preview and photo.

Analysis

For saving the picture in the Biometra-specific BD1 format, JPG or TIF
format and the following transfer to the BDA analysis software. After
saving the gel picture will automatically be opened as black&white picture
in the analysis part

Exit

for further gel analysis.

For closing of the capture window.

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24

Image Capture DSLR


3.2.6 Basic functions

Load image

Images saved in JPG, TIF or Biometra specific BD1 format can be


loaded to the capture window.

Save image

The displayed gel picture is saved in JPG, TIF or Biometra specific BD1
format by typing in a name. Default is BD1 format which generates a
black&white image including image acquisition camera settings. BD1
is standard format in the gel analysis part of the BioDocAnalyze software.

Print image

A print preview window is opened. It is possible to select the desired


printer (DIN A4 printer or thermal printer). Then the displayed gel picture
can be printed.

Print parameter It can be chosen whether the gel picture is printed with or without camera
settings.

3.2.7 The Gel Picture Window

Image

Display of the photo or loaded gel picture.

Shot
Conditions

Setting parameters of the gel photo or the loaded gel file are shown.

Comments

File comments can be entered. These comments are only saved in BD1format files!
The comments are printed below the gel photo and can also be seen in the
BioDocAnalyze analysis window as General Comment.
Please regard: It is only possible to print around 20 chars per line and 5
lines.

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25

Image Capture Compact Camera

4 BDAdigital Image Capture


with Digital Compact Camera,
e.g. PowerShot G10
The BDAdigital image capture software is started with a LEFT MOUSE BUTTON CLICK on the icon digital camera.

When starting the BDAdigital capture software


for the first time after installation you will be
asked for a 4-digit software code to activate
the capture screen.
The code comes along with the dongle.

The window Capture digital camera is opened and a loading bar indicates that the software
just initializes the digital camera.

Fig. 4-1

Window Capture digital camera

The line Camera should show e.g. PowerShot AG10. In case that only Model is shown
the camera is not correctly installed or not switched on. The camera needs to be on replay
and then shows PC on the camera display (display is not existing at all camera models).
When the capture window is opened it starts with the camera settings of the last opened profile.
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26

Image Capture Compact Camera

4.1 The Image Capture


These are the typical steps for image capture:
10. Switch on the live preview:

11. Place the electrophoresis gel on the transilluminator.


12. Switch on the light source of the darkhood.
13. Place the gel with the help of the live preview in the transilluminator center.
14. Choose the desired zoom area by window
Settings:
15. Choose the appropriate settings profile:
16. Take

photo:

17. If necessary optimize the exposure time Tv and the lens aperture Av in window Settings in set Shooting Mode Manual and take another photo.
18. Save and print the

image:

Please see details of the different functions in section 4.2.

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Image Capture Compact Camera

4.2 Functions and Capture Parameters


The window Capture digital camera is widely self-explaining and very similar to general
known parameters in photography. In spite of that the individual functions are explained in
the following.

4.2.1 Profiles with Capture Parameters


Profile

This includes some profiles with working parameters for the image acquisition of
certain gel types.
A mouse click on the profile will set the parameters in the camera. The corresponding parameters are shown in the cards Settings and Advanced. It is essential that
the Shooting Mode is manual otherwise the settings shown in the card Settings
will not really be the used parameters.
It is also possible to enter names for individual settings. After typing in the new
name and setting the parameters the new profile has to be saved .
Switch off of the live image will accelerate the change of profiles.

Save

This saves user-defined profiles under the active profile name.


Before saving you should check whether already a profile with the same name exists because it would be overwritten.

Clear

This deletes the active profile. The Biometra saved profiles can not be deleted.

4.2.2 The Card Settings

Shooting Mode For choice of capture mode. Typical settings are Manual or Auto.
-

Manual

Exposure time and lens aperture can be set in lines Av and Tv. Even
for the use of profile parameters the mode should be Manual.
It should be kept in mind that the camera can not set the largest apertures
(= small aperture number) together with a large zoom factor. In these
cases the camera automatically chooses the largest possible lens aperture. After the picture is taken the aperture display on the card is actualized to the really used one.

Auto

The camera sets the capture parameters exposure time and lens aperture automatically. Be aware that these settings are not displayed in the
camera settings.

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28

Image Capture Compact Camera


Be aware that the displayed and printed settings are not the true settings
the cameras has automatically chosen for the photo!
-

Tv

The camera automatically chooses the optimal lens aperture in relation


to the manually set exposure time. After the picture is taken the automatically used aperture is displayed in the card Settings.

Av

The camera automatically chooses the optimal exposure time in relation to the manually set lens aperture. After the picture is taken the automatically used exposure time is displayed in the card Settings.

Lens aperture, For setting the lens aperture. A small aperture number stands for a wide
open lens, a high aperture number for a more closed lens. The depth of
Av
focus increases with rising aperture number (= smaller lens aperture). Agarose gels, especially thicker gels, should be photographed with high aperture number (= small aperture). Otherwise photos may not be focussed.
Exposure time, For setting the exposure time. The time is to be set in dependence of
sample/illumination and lens aperture. For smaller apertures (= high aperTv
ture number, e.g. 8) exposure times of up to 8 seconds can be necessary
for a photo of fluorescent gels.
Resolution

For choice of image resolution in pixels. The higher the resolution the
bigger the file size.
High resolutions will cause longer data transfer times from camera to PC
on computers with slow processors and memory below 512 MB RAM. For
an efficient operating it is recommended to use a computer with at least 1
GB RAM and a 2.8 GHz processor.

In pixels

PowerShot G10

PowerShot G9

PowerShot
A640

PowerShot
A620/G6

4416 x 3312
3456 x 2592
2592 x 1944
1600 x 1200

4000 x 3000
3264 x 2448
2592 x 1994
640 x 480

3648 x 2736
2816 x 2112
2272 x 1704
640 x 480

3072 x 2304
2592 x 1944
2048 x 1536
640 x 480

High
Medium1
Medium2
Low
Zoom

The optical zoom can be set with the slider or by typing in a value between
0 and 13 (G10, G9), 0 and 8 (A640/A620), 0 and 12 (G6/G5/G3) resp. 1 to
10 (G2).
A higher zoom reduces the amount of light that reaches the camera sensors. This can cause difficulties for the autofocus. When the autofocus
does not succeed to take a focussed picture although there is a clear object in the image center please
-

set a longer exposure time (Shooting Mode Manual)

set less zoom.

Use the function AF Lock for fixation of the autofocus. (see 3.2.5)

use the function manual Focus (MF button on camera back). This
manual focus is not available for use with remote control by the computer. For use of the manual focus please disconnect the USB cable
of the camera from the PC and run the camera separately. Please set
also the macro mode (flower symbol on camera back). The photos are
saved on the compact flash card.

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Image Capture Compact Camera


4.2.3 The Card Advanced

Quality

For choice of compression of picture data in JPG format. In general


quality normal will be sufficient. Quality superfine with only low compression needs more saving capacity and time for image analysis.

ISO

For setting of the sensitivity. Value ISO 400 is recommended for low illumination and big zoom, but in contrast to photos at ISO 50 a certain background noise appears.
In most cases it is advised to use ISO 50. Only for the acquisition of very
faint signals at high zoom factors it can be necessary to raise the sensitivity to ISO 400.

Flash

For activation or deactivation of the flash. Applications with darkhoods


should be done with flash off. Flash on or auto can be used for photographs with stand in a dark room, but reflections on the gel surface can not
be excluded.

Exposure
Compensation

For setting an exposure correction. A fine-tuning of the optimal exposure can be done in small steps.
This function is not available in shooting mode Manual because lens aperture and exposure time are specifically set in the manual mode.

White Balance

For setting the white balance. Colors can be mirrored more true to original when the illumination source is set. This factor is of only minor relevance for black&white photos.

Autofocus
Distance

For definition of distance where the autofocus will look for the sample.
For image acquisition with Biometra darkhoods Close up has to be set.
This setting will lead within the limited distance of camera to gel to wellfocussed pictures over the whole range of zoom.

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30

Image Capture Compact Camera


4.2.4 Camera Settings for Typical Gels
The software provides camera settings for two typical gel types in Profiles. Starting with
these settings it is very easy and fast to optimize the camera settings for individual gels.
Gel type

EtBr Stained Agarose Gel Coloured Polyacrylamide


Gel
on UV table

on UV table with yellow


converter plate, without UV
filter on camera lens,
e. g. silver or Coomassie
Blue stained Polyacrylamide gel

Profile DNA/EtBr

Profile Converter

Shooting Mode

Manual

Manual

Lens aperture Av

6.3

4.0

Exposure time Tv

4s

1/125 s

Autofocus distance

Close up

Close up

ISO

50

50

Flash

Off

Off

Quality

Normal

Normal

Resolution

Medium 1

Medium 1

Zoom

e. g. 5

e. g. 5

Exposure
sation

compen- 0

White balance

Auto

0
Fluorescent

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Image Capture Compact Camera


4.2.5 Further Functions for Image Capture
AF Lock

Function for fixation of the autofocus. This function can be


used for photos which cannot be focussed with the autofocus. This may happen with gels which have no bands or
have only very weak bands in the gel center or when using
a high zoom.
The principle of this function is that first a clear bright tool is
placed in the center and the autofocus is directed to that.
After fixing the autofocus in this position the tool is removed
and the photo can be taken.
Please note:
When you are changing the zoom you have to set the autofocus again!
Procedure:
A. with fluorescent agarose gels:
a) Switch on white light from above (+ place a thin ruler on
the gel),
activate the autofocus button (or take a photo),
activate the AF Lock function,
switch off the white light from above (and remove the
ruler),
switch on the UV light,
take the photo.
b) place a fluorescent ruler on the gel,
activate the autofocus button (or take a photo),
activate the AF Lock function,
remove the ruler,
take the photo.
B. with coloured gels on converter plate:
Place a non-fluorescent ruler on the gel,
activate the autofocus button (or take a photo),
remove the ruler,
take the photo.

Delay

With activated Delay function the camera updates the internal settings with a 5 seconds delay after the last
change of settings parameters in the cards Setting and
Advanced. The use of the delay function is recommended
for a faster operating if the user wants to change several
parameters before taking the next picture.
If it is intended only to change one parameter it is more
practical to deactivate the delay function. Then the camera
will react directly after the parameter on the card is
changed.

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Image Capture Compact Camera


It is possible to manually trigger the updating of internal
camera settings with the Refresh button. Then it is not necessary to wait the 5 seconds standard delay for automatic
updating.

Refresh

Live
on/off

image For switch on/off the live preview in window Live Preview. Due to the high iteration frequency of the picture and
for this reason short exposure times it is possible that the
live preview will not be as bright and focussed as the real
gel picture.

Autofocus

For manual activation of the autofocus. This can be


helpful in case that the camera fails to focus automatically.

4.2.6 Take photo and display settings

Take picture

Click on the button releases the camera. The picture is transferred from
camera to PC and is displayed in the gel window in the right of the Capture
window.
The additional functions Rotate, Invert, Black&White Mode and Saturation are deactivated after taking a photo or printing. These functions have
to be activated again when it is desired to have.

Rotate 180

For rotating the picture 180, for example when the gel is positioned the
opposite way round on the illumination table or when the camera is fixed
on the darkhood or stand with the camera control panel ahead.

Invert

For inverting of the gel picture. The use of this function is only senseful
with black&white pictures.

Black&White
Mode

Activation of this function results in a change of the colour picture to a


grey-scale picture.

Saturation

Activation of this function sets areas of the photo to blue colour if the signal
reaches saturation. The photo display automatically switches to
black&white mode.
The pixels of the area to be quantitatively analyzed later must not be
saturated, neither true white or true black. That means that the area of
interest must not be in blue colour. This can be achieved by shorter exposure times or with smaller lens apertures (= larger lens aperture number).
When using longer exposure times it is possible that the live preview is
darker than the photo. This will cause differences in the saturation display
of preview and photo.
BDAdigital Manual, Vers. 04_11

33

Image Capture Compact Camera


Analysis

For saving of the picture in the Biometra-specific BD1 format, JPG or TIF
format and the following transfer to the BDA analysis software. After
saving the gel picture will automatically be opened as black&white picture
in the analysis part for further gel analysis.

Exit

For closing of the capture window.

4.2.7 Basic functions

Load image

Via the folder icon already saved pictures in JPG, TIF or Biometra specific BD1 format can be loaded to the capture window.

Save image

Via disc icon the active gel picture is saved in JPG, TIF or Biometra specific BD1 format by typing in a name. Default is BD1 format which generates a black&white image including image acquisition camera settings. BD1 is standard format in the gel analysis part of the BioDocAnalyze software.

Print image

A print preview window is opened. It is possible to select the desired


printer (DIN A4 printer or thermal printer). Then the displayed gel picture
can be printed.

4.2.8 The Gel Picture Window

Display of the photo or loaded gel picture.

Image
Shot
tions

Condi- Setting parameters of the gel photo or the loaded gel file are shown.

Comments

The complete parameters are only saved with photos in BD1 files.
File comments can be entered. These comments are only saved in BD1format files!
The comments are printed below the gel photo and can also be seen in the
BioDocAnalyze analysis window as General Comment.
Please regard: It is only possible to print around 20 chars per line and 5
lines.

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34

Service

5 Service
In case you have any problem with the device please contact our service division or your
local Biometra dealer.
Biometra GmbH
Service Department
Rudolf-Wissell-Strae 14-16, D-37079 Gttingen, Germany
Tel:
+49 551 50686-10 or -12
Fax: +49 551 50881-11
e-mail: service@biometra.com
Please follow the return instructions when returning the device:
Return instructions
Please contact our service department for providing a return authorization number (RAN).
This number has to be applied clearly visible to the outer box.
Returns without the RAN will be not be accepted!
Return only faulty devices. For any technical problem that is not clearly identifiable as a
device failure, please contact the Service Department of Biometra.
Use the original packing or a similar robust packing when returning the material.
The darkhood must be shipped on a pallet. The transilluminator has to removed
from the hood and must be shipped separately! The drawer must be secured with
some packing material to avoid that the drawer is moving and touching the UV
protection shield during transport.
Mark the outer packing with CAUTION! SENSITIVE ELECTRONIC INSTRUMENT!
Please include a precise description of the problem and preferably one that also describes
by which procedure the failure occurs or how it is caused.
Important:
Clean every part of the device from residues such as chemical, radioactive and
dangerous biological contamination. Please confirm in writing (Equipment
Decontamination Certificate) before every return that the device is free of radioactive
and dangerous biological contamination. Contaminated devices sent to Biometra will
be refused!
The sender will be liable for the repair order in case of damage resulting from an
inadequate decontamination of the device.
Please include a note with the following information:
a) Senders name and address
b) Contact person and phone number in case of inquiry.

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35

Service

6 Equipment Decontamination Certificate


To enable us to comply with german law (i.e. 71 StrlSchV, 17 GefStoffV and 19 ChemG)
and to avoid exposure to hazardous materials during handling or repair, please complete this
form, prior to the equipment leaving your laboratory.
COMPANY / INSTITUTE ____________________________________________________________________
ADDRESS ________________________________________________________________________________
PHONE NO _______________________________ FAX NO _______________________________________
E-MAIL ___________________________________________________________________________________

EQUIPMENT

If on loan / evaluation

Model

Serial No

__________________

__________________

__________________

__________________

__________________

__________________

__________________

__________________

Start Date: ________________

Finish Date ____________________

Hazardous materials used with this equipment


_________________________________________________________________________________
_________________________________________________________________________________
_________________________________________________________________________________

Has the equipment been cleaned and decontaminated? YES / NO (delete)

Method of cleaning / decontamination


_________________________________________________________________________________
_________________________________________________________________________________
_________________________________________________________________________________

NAME ________________________________

POSITION ___________________________

(HEAD OF DIV./ DEP./ INSTITUTE / COMPANY)

SIGNED ______________________________

DATE _______________________________

PLEASE RETURN THIS FORM TO BIOMETRA GMBH OR YOUR LOCAL BIOMETRA DISTRIBUTOR TOGETHER WITH THE EQUIPMENT.
PLEASE ATTACH THIS CERTIFICATE OUTSIDE THE PACKAGING. INSTRUMENTS WITHOUT
THIS CERTIFICATE ATTACHED WILL BE RETURNED TO SENDER.

BDAdigital Manual, Vers. 04_11

36

Service

General Information for Decontamination:


Please contact your responsible health & safety officer for details.

Use of radioactive substances:


Please contact your responsible person for details.

Use of genetically change organism or parts of those:


Please contact your responsible person for details.

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37

Service

7 Disposal
Due to the application in a laboratory the system must be decontaminated before return as
electronic waste.

Hinweis

fr die Entsorgung von Elektroaltgerten

Note

for disposal of electric / electronical waste

Renseignement

du traitement des dchets des


appareils lectrique / lectronique

Das Symbol der durchgestrichenen Abfalltonne bedeutet fr unsere Kunden in Deutschland,


da dieses Produkt von der Firma Biometra kostenlos zur Entsorgung zurckgenommen
wird.
Zu diesem Zweck kontaktieren Sie bitte unsere Service-Abteilung!
Auerhalb Deutschlands wenden Sie sich bitte an den fr Sie zustndigen Hndler.
Dieses Symbol gilt nur in Staaten des EWR*.
*EWR = Europischer Wirtschaftsraum, umfasst die EU-Mitgliedsstaaten sowie Norwegen, Island und Liechtenstein.
--------------------------------------------------------------------------------------------------------------------------------------------------------------------This symbol (the crossed-out wheelie bin) means, that this product should be brought to the
return or separate systems available to end-users according to yours country regulations,
when this product has reached the end of its lifetime.
For details, please contact your local distributor!
This symbol applies only to the countries within the EEA*.
*EEA = European Economics Area, comprising all EU-members plus Norway, Iceland and
Liechtenstein.
--------------------------------------------------------------------------------------------------------------------------------------------------------------------Cet symbole (conteneur dchets barr dune croix) signifie que le produit, en fin de vie,
doit tre retourn un des systmes de collecte mis la disposition des utilisateurs finaux
en consquence des rgulations par la loi de votre pays.
Pour des information additionel nous Vous demandons de contacter votre distributeur!
Cet symbole sapplique uniquement aux pays de lEEE*.
*EEE = Espace conomique europen, qui regroupe les tats membres de lUE et la Norvge, Islande et le Liechtenstein.
BDAdigital Manual, Vers. 04_11

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