Professional Documents
Culture Documents
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.
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
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
DISPOSAL ..................................................................................................................................... 37
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:
-
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
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.
Note:
Minimizing Dust
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.
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.
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. Mounting of camera
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!).
Installation
2. Covering of lens release
Special screw
3. Security bracket
Special
screw driver
Special
screw driver
Special screws
Security bracket
10
Installation
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
Special screw
Special
screw driver
11
Installation
3. Security bracket
Special
screw driver
Security bracket
Special screws
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.
12
Installation
1.3.1 Overview
!
For installation procedure please refer to following chapters with detailed information.
completed
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!
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.
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>.
********************************************************************
It is also possible to install the BioDocAnalyze software and the drivers of the dongle separately:
BioDocAnalyze
software
Dongle
********************************************************************
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.
16
Start of Program
Gel analysis.
This manual only refers to the image capture with the digital camera.
Gel analysis is described in the separate manual BioDocAnalyze.
17
The BDAdigital image capture software is started with a LEFT MOUSE BUTTON CLICK on the icon DSLR BDAdigital.
The window Capture digital camera is opened and shows the detected camera in line
Camera.
Fig. 3-1
18
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.
19
Please dont start any further functions of the BDAdigital software while the camera is
taking the image which may take some seconds.
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
Clear
This deletes the active profile. The Biometra saved profiles can not be deleted.
20
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
Av
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.
21
Resolution (pixels)
Compression
Approx. 12.2 MP
Approx. 6.3 MP
Approx. 3.4 MP
Approx. 2.5 MP
Fine
Fine
Fine
Fine
ISO
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
22
Live view
on/off
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.
23
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
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.
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
24
Load image
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
Print parameter It can be chosen whether the gel picture is printed with or without camera
settings.
Image
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.
25
The window Capture digital camera is opened and a loading bar indicates that the software
just initializes the digital camera.
Fig. 4-1
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.
BDAdigital Manual, Vers. 04_11
26
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:
27
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
Clear
This deletes the active profile. The Biometra saved profiles can not be deleted.
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.
28
Tv
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
-
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.
29
Quality
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
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.
30
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
31
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.
32
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
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
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
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
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
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.
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.
35
Service
EQUIPMENT
If on loan / evaluation
Model
Serial No
__________________
__________________
__________________
__________________
__________________
__________________
__________________
__________________
NAME ________________________________
POSITION ___________________________
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.
36
Service
37
Service
7 Disposal
Due to the application in a laboratory the system must be decontaminated before return as
electronic waste.
Hinweis
Note
Renseignement