Camera installation and settings

JPK Software Integration
for Cameras
User Manual
Version 2.0
06 / 2012
© 2003-2012 JPK Instruments AG
all rights reserved
Table of Contents
§1
Introduction Words ................................................................................................ 4
§2
Andor Camera ........................................................................................................ 5
2.1 Introduction ...................................................................................................................................................... 5
2.2 Hardware Installation ........................................................................................................................................ 5
2.2.1
Connecting Andor Camera to JPK PC through USB ........................................................................ 5
2.2.2
Installing Andor PCI Board into JPK PC within NanoWizard® Control Station ................................. 5
2.2.3
Installing Andor PCI Board into JPK PC for Vortis™ SPMControl Station ........................................ 7
2.2.4
Water cooling system from Koolance ............................................................................................... 9
2.3 Software Installation ....................................................................................................................................... 11
§3
ProgRes® CCD Camera....................................................................................... 12
3.1 Introduction .................................................................................................................................................... 12
3.2 Software Installation ....................................................................................................................................... 12
§4
ImagingSource® Camera .................................................................................... 12
4.1 Introduction .................................................................................................................................................... 12
§5
µEye® USB Camera ............................................................................................. 13
5.1 Introduction .................................................................................................................................................... 13
§6
Software Overview: JUnicam Image Viewer ...................................................... 14
6.1 Introduction .................................................................................................................................................... 14
6.2 JUnicam Main Window ................................................................................................................................... 14
6.3 JUnicam Software Version ............................................................................................................................. 15
6.4 Saving Images................................................................................................................................................ 15
6.5 Recording Image Sequences or Videos ......................................................................................................... 16
6.6 Splitting Videos into Single Images ................................................................................................................ 17
6.6.1
Using Ubuntu: ................................................................................................................................. 17
6.6.2
Using Windows: .............................................................................................................................. 17
6.7 Other Software ............................................................................................................................................... 17
§7
6.7.1
ImageJ ............................................................................................................................................ 17
6.7.2
Mplayer / Mencoder ........................................................................................................................ 18
Camera Settings .................................................................................................. 18
7.1 Introduction .................................................................................................................................................... 18
7.2 Adjusting Camera Settings ............................................................................................................................. 19
7.3 Camera Settings - Andor ................................................................................................................................ 21
7.4 Camera Settings - ProgRes® Camera ........................................................................................................... 22
7.5 Camera Settings - ImagingSource® ............................................................................................................... 23
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JPK Software Integration for cameras - User Manual v2.0
§8
TTL Trigger for Image Acquisition ..................................................................... 24
8.1 Hardware Connection .................................................................................................................................... 24
8.1.1
Andor Camera ................................................................................................................................ 25
8.1.2
ProgRes® Camera ......................................................................................................................... 26
8.1.3
ImagingSource® Camera............................................................................................................... 26
8.2 Software Configuration .................................................................................................................................. 27
§9
Camera Adapters ................................................................................................. 29
§1
Introduction Words
This manual is mainly dedicated to introduce the camera integration into JPK Instruments systems. There are three
camera systems that are fully integrated in the Software of JPK NanoWizard®, CellHesion200™ and NanoTracker™
systems. It should be explained, how the Andor cameras, ProgRess® CCD cameras, ImagingSource® CCD
cameras, and µEye® USB cameras can be connected to the JPK Instrument systems and how they can be operated
via the JPK software. The main camera manual should be always the provider instructions of the camera itself.
Most NanoWizard® AFM systems are equipped with a Firewire camera. The same camera can be used
with either an inverted optical microscope (Life Science system) or the top view optics (standard system).
If using an inverted optical microscope with the optional DirectOverlay feature, the optical image can be
imported into SPM (see Main Manual Section Fehler! Verweisquelle konnte nicht gefunden werden.)
Simply connect the Firewire cable, or USB cable from the AFM computer to the camera. Consider “video”
labelled Firewire/USB ports. The connection will automatically be recognized by the software.
Start the camera viewer with the CCD button from within the JPK SPM software icon bar. The software
for the optical camera is called JUnicam.
The software should automatically recognize the camera type and settings (this may take 1-2 seconds).
The camera window will automatically display the live camera image.
Generally no further settings are required – the camera electronics will make an automatic adjustment of
gains and exposure time that will display a reasonable image in most circumstances.
Note that the default size of the camera window is smaller in pixels than the camera chip size. This is for
convenience, so it does not cover too much of the screen. The window can be increased up to the size
of the chip, thereafter the image panel will not increase in size. The saved images always have the full
chip size, regardless of the display size.
Please connect the USB-camera to the “video” labelled USB-port of your JPK-PC. In any other case it
could be that the performance of the camera will be influenced.
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JPK Software Integration for cameras - User Manual v2.0
§2
Andor Camera
2.1 Introduction
The CCD cameras from Andor Technology can be integrated into the JPK software.
The following requirements should be met:
1.
A license for the Linux version of the Andor Software Development Kit (SDK) is a prerequisite, which is part
of the software integration package that can be purchased through JPK Instruments.
2.
If applicable to the specific Andor camera, the corresponding Andor PCI interface board needs to be
transferred to the JPK PC. Obviously this requires a free PC slot, yet this should have been verified with
JPK Instruments before the Andor software module was purchased. If doing this yourselves on an existing
JPK PC, a few seals on the controller need to be breached. The next section deals with this hardware
installation.
3.
Andor camera support requires JUnicam instead of Unicam as the camera application. For Unicam users,
adapting to JUnicam there should hardly be any noticeable differences. A JUnicam manual is included in
this document.
Note: It is important to realize that some functions of the Andor camera may not (yet) be fully supported in the JPK
software interface. In case of doubt, please contact JPK Instruments at [email protected]
2.2 Hardware Installation
The main guide for hardware installation should always be the installation guide of the camera
itself. This section focus on installation of Andor equipment into JPK PCs.
2.2.1
Connecting Andor Camera to JPK PC through USB
When the Andor camera to be interfaced with the JPK software is USB interfaced (such as the Andor Luca® or the
Andor Clara® series), simply connect the USB cable to an available USB port on the JPK PC; preferably on the back
side of the PC. No further JPK-specific hardware installation is required and the rest of this chapter can be skipped —
please refer to the Andor hardware manual for further information.
2.2.2
Installing Andor PCI Board into JPK PC within NanoWizard® Control Station
When starting to use an Andor camera with a PCI interface board in the JPK software, the PCI board first needs to be
transferred to the JPK PC. This section describes this procedure for standard JPK Control Stations.
Open the PC
To open the PC, first shut down the PC entirely (including the toggle switch on the power supply on the rear side and
disconnect all cables (see left image below). Protect the light guide cable as described in the hardware section of
your main JPK product manual. Release the four screws that attach the PC to the 19-inch rack (see middle image
below). Now pull the PC out of the rack.
Important:
-
You will have to breach a few safety seals in taking out and opening the PC.
-
Mind that the PC weighs about 15 kg — do not slide the PC out solely by its handles. Instead, support the PC in
the middle as well.
1. Disconnect all cables.
2. Release screws on front side.
3. Slide PC out of Control Station.
To open the PC cover, unscrew its 6 screws and slide the cover backwards while lifting it. Details of the PC cover
may depend on the exact PC model.
4. Open PC cover.
Install the Andor PCI board
Locate a free PCI slot on the motherboard in the section indicated in the
image on the left.
Since the standard Andor PCI boards are quite large, other boards may have
to be shifted for the Andor board to fit appropriately.
If so agreed with JPK Instruments, you may have to remove an existing PCI
board at this point (such as an RS232 serial port board) to make space.
Only when moving the existing
JPK DSP board:
Release the securing bracket and
take it off.
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JPK Software Integration for cameras - User Manual v2.0
Release the clamping screw on the
DSP board and carefully remove it
from its PCI slot from under the
traverse.
Carefully put the DSP board in a new PCI slot and fix it to the PC housing
using its screw. Secure the board by attaching the bracket to the traverse.
As soon as a free PCI slot is available, the Andor PCI board can be installed.
To the left, the Andor CCI-23 (the default interface board for the iXon camera
range) is shown.
Note: Please follow the instructions exactly as explained in the Andor
manual! In particular: if so advised, make sure to attach an additional
power cable from the PC power supply to the Andor PCI board.
Close the PC
Close the JPK PC and reinstall it into the Control Station by following the steps under ‘Open the PC’ above in the
reverse order.
Connect the Andor camera to the PC
To connect the Andor camera to the PC, again please follow the instructions found in your Andor hardware manual.
2.2.3
Installing Andor PCI Board into JPK PC for Vortis™ SPMControl Station
The procedure is similar to chapter 2.2.2. The main difference is that the PC is a stand alone system.
Open the PC
To open the PC, first shut down the PC entirely (including the toggle switch on the power supply on the rear side) and
disconnect at least the power cable.
Install the Andor PCI board
Locate
a
free
PCI
slot
on
the
motherboard (1- for PCI = CCl-23, 2 –
PCIe (express) = CCl-24) in the section
indicated in the image on the left.
Since the standard Andor PCI boards
1
2
are quite large, other boards may have
to be shifted for the Andor board to fit
appropriately.
Blue circles – connect the fly lead, and
splitter lead on the right place
Red circle – information about model
number
PCI
board
(CCL-23)
or
PCIe = XX
Carefully put the board in a PCI slot and
fix it to the PC housing using its screw.
Secure the board by attaching the
bracket to the traverse.
Close the PC and connect all cables.
Follows the instruction from Andor to
connect the camera.
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JPK Software Integration for cameras - User Manual v2.0
The e.g. iXon detector cable has to be
connected to the camera as well as to
the PCI board.
Note: Do not use the camera
without the fan power supply.
2.2.4
Water cooling system from Koolance
Some of the Andor cameras can be equipped with a water cooling system. This chapter describes the basic steps to
install and use the water cooling system from Koolance Inc.
Please read the installation instruction for the water cooling system carefully.
Consider and follow the advices and information of Andor for use of water cooling systems.
Main parts are:
-
Koolance Exos cooling system
-
2 tubing adapters (Festo; plug-screw connector, QS-1/4-6, for OD tubing 6mm)
-
Tubing 2x5 m (Festo; polyurethane, PUN-H-6X1-BL, OD 6mm, ID 4mm)
Installation steps:
Switch off the JPK PC, disconnect the
1
power supply.
Install the Koolance slot adapter [1]
according to the Koolance user’s manual.
3
The cooling system requires 12V DC and
approximately
30W.
Therefore,
the
internal power supply can be use [2].
The PCI express board for the Andor
camera [3] is visible left from the slot
adapter.
2
Mount the FESTO tubing adapters into the
threaded sockets of the cooling box. For
improved sealing use PTFE tape (0.1mm
thickness).
Insert the tubing into the FESTO tubing
adapters. JPK support the delivery with
2x5 m tubing.
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JPK Software Integration for cameras - User Manual v2.0
Plug as far as it will go both tubings into
the related nozzles of the Andor camera.
After assembly of the tubing and the
cooling system please fill the Koolance
systems with liquid.
2.3 Software Installation
The JPK Andor software integration module should be purchased through JPK Instruments. All required software
components will then automatically be included in the next software release, which can be downloaded from the
JPK customers website (http://customers.jpk.com).
Note: it is not necessary to install separately the Andor SDK. In some combinations this can induce some
software conflicts with JUnicam.
In particular, three Andor-specific packages are included in the installer:
andordrvlx-dkms_###.deb
Andor Camera driver for Linux
libandor2_###.deb
Packaged Andor Software Development Kit (SDK)
ucandor_###.deb
Unicap driver layer for Andor SDK
Here, ### represents the version number.
In case problems occur during the installation, please contact JPK by email at [email protected]k.com or by phone at
+49 30 5331 12070. Please be prepared to provide any error messages that may have occurred.
§3
ProgRes® CCD Camera
3.1 Introduction
The ProgRes® CCD cameras from Jenoptik can be integrated into the JPK software.
1.
JPK supports MF/CF cameras as well as MF
coo
l/CFcool Firewire cameras. Additional requirements are not to
be considered.
2.
Jenoptik provides image capture software “ProgResCapturePro” which can be installed on a WindowsPC or
MAC.
Note: It is important to realize that some functions of the ProgRes® camera may not (yet) be fully supported in the
JPK software interface. In case of doubt, please contact JPK Instruments at [email protected]
3.2 Software Installation
The JPK ProgRes® software integration module should be purchased through JPK Instruments. All required software
components will then automatically be included in the next software release, which can be downloaded from the
JPK customers website (http://customers.jpk.com).
Note, that it is not necessary to install separately the ProgRes® SDK. In some combinations this can induce some
software conflicts with JUnicam.
Make sure that your camera is with the right firmware version – actually JPK supports the Jenoptik
firmware 4.2 (13.07.2011).
If the firmware is too old or too new it can be that some features will not be supported.
In case problems occur during the installation, please contact JPK by email at [email protected] or by phone at
+49 30 5331 12070. Please be prepared to provide any error messages that may have occurred.
§4
ImagingSource® Camera
4.1 Introduction
The JPK ImagingSource® software integration module should be purchased through JPK Instruments. All required
software components will then automatically be included in the next software release, which can be downloaded
from the JPK customers website (http://customers.jpk.com).
Note: it is not necessary to install separately the ImagingSource® SDK. In some combinations this can
induce some software conflicts with JUnicam.
The Trigger function is available for e.g. FireWire cameras of the DFK 31BF03, DMK 31BF03, DFK 41BF02 family.
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§5
µEye® USB Camera
5.1 Introduction
The JPK µEye® software integration module should be purchased through JPK Instruments. All required software
components will then automatically be included in the next software release, which can be downloaded from the
JPK customers website (http://customers.jpk.com).
Actually, only for some cameras of the µEye family the compatibility to JPK software was tested
-
UI 1240 LE-M-GL (CMOS, 1280 x 1024, 6.784 x 5.427 mm, 25fps, Pixelsize 5.3µm,1/1.8"
-
UI 1645 LE (CMOS, 1280 x 1024, 4.608 x 3.686 mm, 25fps, Pixelsize 3.6 µm, 1/3"
-
UI-LE1488-M (CMOS, 2560 x 1920 QSXGA/5 MP, 5.632 x 4.224 mm, 6fps, Pixelsize 2.2µm, 1/2"
The Trigger function is available for e.g. UI-1240 ME-C or similar cameras.
If you want to use any other model of the camera family please contact JPK Instruments.
Note: it is not necessary to install separately the µEye® SDK. In some combinations this can induce some
software conflicts with JUnicam.
§6
Software Overview: JUnicam Image Viewer
6.1 Introduction
An important component of the JPK Control Software is the live optical image viewer, called JUnicam. JUnicam
allows live display of the current microscope-mounted camera image at video rate for a range of cameras including
Andor, as well as useful interactions with the JPK software.
JUnicam can be started from the shortcut icon bar, or by selecting CCD Camera from the Camera menu.
6.2 JUnicam Main Window
When started, JUnicam automatically searches for supported cameras attached to the PC. In all screenshots and
corresponding descriptions below, an Andor iXon+ 897E camera (model DU-897E-C00-#BV) was used. Other
actively supported cameras include several from JenOptik, Imaging Development Systems (IDS), and The Imaging
Source. Please contact JPK for further enquiries under [email protected] or call +49 30 5331 12070.
The currently used camera is displayed on the top left. If more than one camera was found, the corresponding drop
down menu can be used to select another camera. Just like in other JPK software, JUnicam has a shortcut toolbar
which gives access to its most frequently used functions. In the right top corner, the current frame rate (in frames per
second or fps) is shown.
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JPK Software Integration for cameras - User Manual v2.0
If problems occur with the displaying of the camera image, the first troubleshooting step should be to
press the Rescan button, which restarts the search for connected cameras.
Right clicking with the mouse in the image will open the menu shown on the right. A few
functions are accessible through this menu. Using Copy will copy the current frame the
clipboard, to be pasted into another program.
The 1:1 item will scale the JUnicam window to render every camera pixel on a single
monitor pixel. When expanding the PC’s desktop over two monitors, Fullscreen mode will
expand the window over a single monitor.
6.3 JUnicam Software Version
As an independent Java application, JUnicam has its
own software version numbering. The current version
can be found by clicking on the About button. This
version number will be useful when contacting JPK
Instruments for support.
JUnicam implements a graphical user interface for
Unicap camera drivers, the installed version number of
which is also displayed.
6.4 Saving Images
Still images can be stored from JUnicam by using the Save and Save as buttons in the
toolbar. The difference between the two is that the Save button allows for saving images with
automatically incrementing filenames. The Save as button will always open a dialog box.
If no image has been saved during the current
JUnicam session, both Save buttons will open
the dialog shown. Images can be stored in
JPEG, PNG, TIFF or BMP formats, selected
from the drop-down menu.
In the shown case, consecutive usage of the
Save button will create filenames image.tif,
image1.tif, image2.tif, etc.
Using the save buttons, images are stored exactly as displayed on-screen, including contrast enhancements.
Note: Only the TIFF and PNG file formats allow storing data from cameras with a higher bit-depth than 8-bits
such as from the typical 14-bit or 16-bit channels of an Andor camera.
6.5 Recording Image Sequences or Videos
Apart from still images, JUnicam can also be used to store image sequences with a fixed time interval, or
even stream videos to disk into a single video file.
The desired video format is selected using the
Files of Type drop down menu.
Selecting any of the still image formats will start
the recording of an image sequence. The rate at
which images should be captured can be
selected.
With the software version 4.0.2xx JPK supports
also selected image acquisition. This mode is
very useful in case of TTL-trigger supported
video acquisition (see chapter § 8).
If the Ogg Theora Video format is selected,
videos can be streamed to disk at the same rate
at which they are being captured (up to 15 fps
using most Firewire cameras).
The Quality setting allows control over the
compression of the Ogg video file; setting it to
the maximum value will store an almost lossless
video.
The video size can be reduced by binning pixels
using the Reduce Size by a factor of control.
Note: This feature is currently experimental.
AVI (uncompressed) video files allow video recording without losses due to compression. Note that thus stored video
files rapidly become extraordinarily large.
During the recording of a video, the Record button will appear as activated, and details about the recording are
displayed in the bottom strip of the JUnicam window. To stop the recording, press the Record button again.
Please NOTE: Recording a video will only save the video with default settings of the JUnicam
software. Any kind of video correction, e.g. contrast enhancement done with the JUnicam
software will NOT be saved.
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6.6 Splitting Videos into Single Images
Performing long term measurements it might be easier to record a video instead of single frames. The following
paragraphs provide a brief description of how to split this video into single frames.
6.6.1
Using Ubuntu:
Once the data is recorded as an .avi-file using the JPK software, it is possible to have a look at the video with
MPlayer or VLC Media Player. Simply open any of those programs and load the file. Make sure MPlayer is installed,
because this will be the program which is used to split the video into single frames. To do so proceed as follows:
•
Open a terminal window
•
Go into the folder where your video is stored
•
Type into the command line: ‘mplayer <filename.avi> -vo png’
The video is automatically split into single frames and stored within the same folder like the video. Other output
formats which are possible are .jpeg or .gif, but since the .png format offers lossless compression it is therefore
recommended.
The ‘mplayer video output’ (-vo) command provides a lot more settings. For additional adjustments like e.g. the
output directory or advanced video processing please see the manual of the ‘mplayer’ command.
6.6.2
Using Windows:
Once the data is recorded as an .avi-file using the JPK software, it is possible to have a look at the video with
MPlayer or VLC Media Player. Simply open any of those programs and load the file. If it is necessary to do the video
processing on a Windows machine, first copy the video to a Windows PC. To make sure the data is not corrupted
play the video once more using VLC Media Player for Windows. The next step is to install VirtualDub
(http://www.virtualdub.org) a program that will do the separation of the single frames. Simply download the file and
unpack it into a new folder. The software can now be started by double-clicking on the file ‘Veedub64.exe’. When all
the software necessary is installed proceed as follows to split the video into single frames:
•
Start the software as described above
•
Open the video with ‘File -> Open video file …’
•
Now save the video in single frames with ‘File -> Export -> Image Sequence’
•
Choose a file name, a directory and an output format and press OK
The video is automatically split into single frames and stored within the chosen folder. Other output formats which are
possible are .jpeg or .bmp, but since the .png format offers lossless compression it is therefore recommended.
6.7 Other Software
A few software packages not maintained or provided by JPK are available that may be useful when analyzing image
or video data.
6.7.1
ImageJ
It may be convenient to use the GNU-licensed software application ImageJ (http://rsbweb.nih.gov/ij/) for processing
of images and videos. ImageJ is also available for Ubuntu Linux and can be installed on the JPK PC. A recent
version that was tested successfully by JPK is release 1.43l, which can be downloaded as a so-called Debian
package from the web. Please contact JPK for further assistance.
6.7.2
Mplayer / Mencoder
Recorded Ogg videos (*.ogv) can be converted to other video formats (*.avi, *.mpg, *.wmv, etc.) using many freeware
video conversion tools that can be downloaded from the internet. A good choice is the utility mencoder, which may
be installed on the JPK PC by logging in as jpkroot, opening a terminal window and entering:
apt-get install mencoder
To convert a file INPUT.ogv to the widely used AVI format (filename OUTPUT.avi) using the DivX codec, type:
mencoder -ovc lavc -lavcopts vcodec=mpeg4 INPUT.ogv -o OUTPUT.avi
See the mencoder manual for more information.
§7
Camera Settings
7.1 Introduction
This chapter contains the description for the Andor cameras. For the ProgRes® cameras from Jenoptik as well as for
the ImagingSource cameras some specifications can be very different or can be not available. In case of any doubt
please read the information of the corresponding camera user manual.
When imaging using a CCD camera in low light level conditions, the key parameters of interest for the user (frame
rate, image brightness, signal-to-noise ratio) are determined by a number of settings:
1.
2.
Fixed camera properties:
a.
sensor size / number of pixels
b.
quantum yield (efficiency of photon to electron conversion)
c.
digitization rate of analog to digital converter(s) (ADCs)
d.
dynamic range / digitization bit depth
e.
inherent noise sources (depends on most of the above properties)
Adjustable camera settings:
a.
sensor cooling
b.
exposure time
c.
camera gain (cf. electron-multiplication gain (EM gain) such as built into many Andor cameras)
d.
pixel readout speed (when multiple ADCs available)
e.
camera readout mode (e.g., frame transfer)
f.
total number of pixels (can be reduced from full chip by pixel binning or region of interest selection)
Obviously, of additional importance is the optimization of the light source that is to be imaged. In the case of low lightlevel fluorescence imaging, a delicate balance has to be found between:
1.
fluorescence excitation power (related to photobleaching)
2.
frame rate
3.
signal-to-noise ratio in the image
It is important to familiarize oneself with the above terms when using high-end cameras such as those from Andor
Technology. In particular, some understanding of noise sources in (EM) CCD imaging is important. More information
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JPK Software Integration for cameras - User Manual v2.0
on these and similar issues related to sensitive CCD camera usage can be found online in many tutorials and other
web resources (e.g., http://www.emccd.com), or in the documentation of the Andor camera.
7.2 Adjusting Camera Settings
A few settings for the Andor camera are available as drop-down menus
directly underneath the camera selection box: the bit depth and pixel binning
settings. Note that changes in the bit depth may automatically affect other
settings such as the selected ADC speed.
All further camera settings can be adjusted by opening the separate Settings panel from the toolbar.
The settings panel opens in the Exposure tab. The
Exposure Time is the main determinant for the frame
rate. In addition, the image brightness scales linearly
with this parameter. Depending on some other settings,
the actual frame rate is additionally influenced by the
pixel readout scheme used. This actual rate is displayed
as well.
The Frame transfer toggle button controls whether the
frame transfer feature is active. When active, acquisition
of a new image can start immediately after the last one,
as frame readout takes place ‘in the background’. Note
that in this case the Exposure Time should exceed the
readout time – the value is automatically corrected.
The option Baseline clamp is only relevant when acquiring long kinetic series – please see the corresponding section
in the Andor manual. The EMCCD Gain is set in the Exposure tab, too. Note that its value only affects the image
when the corresponding ADC channel is selected in the Transfer tab (see below).
The Trigger mode can be used to trigger the camera with either its internal trigger signal (i.e. timing determined by
software settings) or any of the external trigger modes available for the selected camera. The image shows the
options for an iXon camera; see the Andor manual for further details.
The Transfer tab contains all settings related to the
digitization of the image.
For most Andor cameras, the Output Amplifier can be
switched between the conventional readout channel and
the Electron Multiplying channel, to which the EM Gain
setting from the Exposure tab applies.
Depending on the camera model, the ADC readout rate
can be selected from a few options. In the case of the
model used for the screenshots in this manual, the Andor
iXon 897E, the EM channel is equipped with 10, 5, 3 (all
14 bit) and 1 MHz (16 bit) ADCs.
Although a faster readout rate allows a higher frame rate (as the readout time per frame is shorter), one should realize
that faster ADCs generate more readout noise. It is important to keep these dependencies in mind when setting up an
experiment. Again, more detailed information is found in the Andor manual.
The Amplifier gain can in principle always be set to the maximum value. Both Vertical speed and Vertical clock
voltage will not be needed for normal operation. For more information on these properties, please see corresponding
sections in the Andor manual.
A few geometrical operations can be performed to the images read in: flipping or 90° rotations. One will in principle
always want to work in the orientation that fits with the real-world microscope orientation. The horizontal flipping option
is most useful when switching between conventional and EM gain channels (when available), as all pixels in a row are
digitized in opposite order for these channels. This property, related to the mechanical layout of the camera, gives rise
to an unwanted horizontal flip.
The Shutter tab is mainly relevant when using a camera
which has an internal mechanical shutter.
In additional, when using an external shutter, the
parameters in this tab can be used to choose the right
trigger settings.
See the Andor manual for more information on this
feature.
In the Cooling tab, the cooling settings for the Andor
camera can be entered. Cooling of the camera sensor
may significantly enhance the signal-to-noise ratio, which
is why most Andor cameras have this built-in.
When enabled, the Temperature status indicates
whether the control loop is ‘stabilized’ or not – when
indicating ‘not reached’ or ‘not stabilized’, one should
wait until this is the case for best results.
The Temperature setpoint indicates the temperature
the sensor should be cooled at. Please refer to the
camera specifications for details.
The Measured temperature is indicated only when no acquisition is running. This means
that one has to temporarily pause the current acquisition using the Pause button in the
JUnicam toolbar to visualize the actual temperature.
The Shutdown cooler mode determines whether the camera cooling stays on when the software is shut down.
Using the Fan mode drop-down menu the user can select the state of the fan that
cools the camera electronics (not the sensor itself!). If the microscopy application
requires this for stability reasons, one can temporarily switch the fan off.
If switched off for too long, the electronics may become too hot and the camera may produce a sound alarm. See the
Andor manuals for more information on this. Switching off the fan for extended periods of time is only allowed when
using a camera cooled using a water recirculator.
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The Image Display tab contains further parameters that
only change the display and storage behavior of the
image rather than physical camera parameters. The
display contrast can be tuned by changing the Minimum
and Maximum color values. The Auto Adjust button
for the color value range is useful to quickly find the right
contrast settings.
These contrast values directly affect the values in image
files (video files are NOT affected) that are stored by
JUnicam.
(Note that the difference between the settings on this tab
and those in the other tabs is that here only displayspecific; no device-specific settings are shown.)
Camera settings may be saved and loaded on the
Presets tab. The parameters of all tabs will be stored.
After clicking on the + button, a dialog will pop up which
allows to type a name to describe the current settings
(e.g., ‘fluorescence’ or ‘all manual’). This text will then be
displayed in the presets list, which allows to rapidly and
reproducibly switch between sets of values.
The stored presets are retained when the program is
closed.
7.3 Camera Settings - Andor
To run TTL-trigger supported image acquisition 1) the Andor camera has to be connected via TTL-trigger input, 2)
the Trigger mode has to be set to External, and 3) the video capture has to be set to “Capture every x.. th image”.
Change the trigger mode from Internal to External.
“Capture image every xxx seconds” – in that
configuration the video sequence starts with the first
TTL- trigger. Therefore, only one trigger signal is
necessary for each sequence. To stop the image
sequence click on the “Record” button
.
“Capture every xxx image” – in that mode every TTLpulse will induce an image acquisition. Click the
“Record” button again to stop the sequence.
7.4 Camera Settings - ProgRes® Camera
TTL-trigger supported image acquisition is quite similar to Andor: 1) the ProgRes® camera has to be connected via
TTL-trigger input, 2) the Trigger mode has to be set to e.g. Trigger on Rising Edge, and 3) the video capture has
to be set to “Capture every x.. th image”.
Change the trigger mode from Free Running to Trigger
on Rising/Falling/Any Edge.
.
“Capture every xxx image” – in that mode every TTLpulse will induce an image acquisition. Click the
“Record” button again to stop the sequence.
Some ProgRes® cameras allow to send a Trigger out signal (see pin connection in 8.1). The camera settings has to
be changed for Trigger Output to e.g. on “high during Exposure”. To display the output trigger the Precision 6 channel
of ANALOG IN can be used. The example monitors trigger in signal (in blue) and corresponding trigger output
signals (in red).
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7.5 Camera Settings - ImagingSource®
TTL-trigger supported image acquisition is quite similar to Andor and ProgRes®: 1) the Trigger mode is set from
“free running” to “mode 0”, 2) the Trigger polarity has to be set to e.g. Falling Edge or Rising Edge, and 3) the video
capture has to be set to “Capture every x.. th image”.
Change the trigger mode from free running to mode 0;
Trigger polarity: Falling or Rising Edge.
.
“Capture every xxx image” – in that mode every TTLpulse will induce an image acquisition. Click the
“Record” button again to stop the sequence.
§8
TTL Trigger for Image Acquisition
TTL (transistor-transistor logic) devices are wildly used in lots of electronic applications and can be used to
synchronize the NanoWizard AFM with external hardware components like cameras. A particular characteristic of
TTL signals is that they can switch between a low state (below 1 V for a digital 0) and a high state (above typically 3.3
V for a digital 1) in a high switching speed. This is called level change. A combination of a fast switch between low
and high state leads to a pulse segment.
8.1 Hardware Connection
The Vortis controller unit for the JPK NanoWizard III can be equipped with and without a signal access module
(SAM). The full range of TTL control elements can only be used with the signal access module.
NanoWizard® controller without SAM
NanoWizard® controller with SAM
TTL Signal without SAM
The access to the TTL signal is given at the back of the controller via a Sub-D 25 female pin assignment (marked in
green). The standard Vortis controller without signal access module offers the possibly to use two TTL outputs
(marked in red).
Extension mixed signal Sub-D 25 female pin assignment:
Pin
Assignment
1-2
TTL (level change)
Note: The TTL outputs (Pin 1/2) can switch between high and low state (level changer), but there is no possibility to
generate automatic pulses.
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TTL Signal with SAM
The access to the TTL signal is given at the signal access module of the controller via a Sub-D 15 female pin
assignment (marked in green). Next to the switches between high and low state, automatic pulses can be generated.
Furthermore TTL pulses can be synchronized with AFM measurements through pixel, line and frame clocks.
Extension mixed signal Sub-D 15 female pin assignment:
8.1.1
Pin
Assignment
1-2
ground (no TLL output)
3
TTL (level change, pulse)
4
TTL (level change, pulse, frame clock)
5
TTL (level change, pulse, line clock)
6
TTL (level change, pulse, pixel clock)
7-9
ground (no TLL output)
9-11
TTL (level change)
12
ground (no TLL output)
13-15
TTL (level change)
Andor Camera
Use the SMB to BNC cable from Andor.
Connect the SMB-cable to the external trigger port of the
camera.
8.1.2
ProgRes® Camera
Please follow the instructions of the ProgRes® user manual. To connect the Trigger port of the Jenoptik camera the
plug connector RKMCK4 (www.lumberg.de) is needed.
Trigger/Flash
Camera male plug
Typ: Lumberg RSMESD 4 pin
Female plug socket
8.1.3
ImagingSource® Camera
The ImagingSource® cameras can be simply triggered
with a standard BNC-cable.
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8.2 Software Configuration
To monitor the TTL signals with JPK software tools it is necessary to activate:
1.
Channel Setup/Inputs/Precision 5 (if the signal input is Precision 5)
2.
Open the Real Time Oscilloscope/Channel saving – activate Precision 5
To send a TTL signal it is possible to use any of the following options:
3.
SPM Jython console and type in:
a.
dspManager.setDigitalOutPin(0,1,True) to switch on the TTL pulse
b.
dspManager.setDigtalOutPin(0,1,False) to switch off the pulse for pin10 = PT1 at the TTLoutput plug
4.
ExperimentPlanner with an example script e.g. ”TTL-multiple.py”
5.
TTL control via TTL control panel and with Force RampDesigner™ (see NanoWizard main manual
sections 8.4.2. and 8.4.3, or CellHesion 200 manual section 4.11.; the
TTL control panel is NOT yet finished for the NanoTracker™)
Channel Setup
Channel saving of Real Time Oscilloscope
Jython commands to activate and de-activate the TTL
pulse. In this example the pin 9 = PT0 was used for
output.
Real Time Oscilloscope to monitor the TTL-pulse.
ExperimentPlanner – this example uses a TTL trigger to
force spectroscopy on a grid at the beginning of each
force curve.
In that example for each grid point 3 force curves will be
collected.
The Real Time Oscilloscope displays the corresponding
sequence of TTL-signals for 3 force curves per grid
point.
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§9
Camera Adapters
C-mount adapters are necessary to assemble the camera on the camera-port of the microscope body. These lens
couplers can have different magnifications. The right optics depends on the chip size of the used camera.
The following couplers can be used exemplarily for the different camera types:
1)
ImagingSource® camera
e.g. DMK 31BF03, DFK 31 BF03
1/3" chip = 0.3x or 0.5x coupler
2)
ProgRes® camera
e.g. MFCool, CFCool
2/3" chip = 0,63x or 0.7x coupler
3)
Andor camera
e.g. Ixon 897, Clara, Luca
1" chip = 1x coupler (without internal lens)
1/3" chip 1/3 inch chip = 0.3x or 0.5x coupler
Note: the C-mount adapter will change the magnification, e.g. using a 0.6x coupler for the ImagingSource®
camera instead of the standard 0.5x coupler the object within the camera image appears slightly increased
as compared to what is visible within the eyepieces.
Note: All trademarked names mentioned in this manual remain the exclusive property of their respective owners.
JPK Instruments AG
Bouchéstrasse 12
12435 Berlin
Germany
Tel: +49 30 5331 12070
Fax: +49 30 5331 22555
[email protected]
www.jpk.com
JPK-DOC0073
All rights reserved.
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