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Zeiss AxioCam MR Installation And Reference Manual
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Zeiss AxioCam MR Installation And Reference Manual

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Number of this manual: M 60-3-0014 e
Printed 12.2008

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Summary of Contents for Zeiss AxioCam MR

  • Page 1 Number of this manual: M 60-3-0014 e Printed 12.2008...
  • Page 2 Carl Zeiss or that these are not known to Carl Zeiss due to gross negligence and that furthermore Carl Zeiss has for these reasons refrained from eliminating these errors or inaccuracies appropriately.
  • Page 3 The referenced Software of Carl Zeiss ("Zeiss Software"), contained in this documentation, was designed, realized, verificated, validated and released in a certificated process environment. The quality management system is certified following the rule of DIN EN ISO 9001. The fields of application of the Software are common tasks and applications in microscopy respectively imaging (so called "Off-The-Shelf Software").
  • Page 4 EU directives. • Please contact your Carl Zeiss sales/service organization for details relating to disposal and recycling. • This product must not be disposed of with domestic waste or using municipal waste disposal services.
  • Page 5 Installing the camera driver with the hardware wizard ....20 Installing the camera driver using the setup program ....23 How to correct the driver entry in the device manager..... 27 Resetting the AxioCam MR firmware ........29 AxioCam MR Installation + Reference...
  • Page 6 Table of Contents 1.3 Notes on Maintenance..............30 Camera electronic................. 30 Optical system ................30 Cleaning the infrared barrier filter..........31 Important note on the use of C-mount objectives......31 2. Image Acquisition ................32 2.1 General................... 32 2.2 Quick Guide to the First Image with AxioVision....... 33 The workflow Standard..............
  • Page 7 3. Trouble Shooting ................. 75 3.1 Software..................75 3.2 Image Quality ................. 76 4. Technical Data ..................77 4.1 AxioCam MRc (color version) ............77 4.2 AxioCam MRm (monochrome version)..........79 4.3 Spectral Sensitivity ................81 AxioCam MR Installation + Reference...
  • Page 8 FireWire connection via FireWire interface PCI cards rather than the onboard FireWire interfaces. Alternatively, a FireWire hub can be connected between the camera and PC. Carl Zeiss is unable to accept any liability for damage that results from failure to comply with these safety recommendations.
  • Page 9 To make it easier for you to set up the camera, please follow the instructions in these chapters step by step. In this manual the interface between AxioCam MR and the computer is called ® FireWire. Synonym the terms IEEE 1394 a and i.LINK are also used for this interface.
  • Page 10 Limitation of liability No warranty shall be assumed by Carl Zeiss during the warranty period if the equipment is operated without observing the safety regulations. In any such case, Carl Zeiss shall be exempt from statutory liability for accidents resulting from such operation.
  • Page 11 (radiators, stoves). Overheating can cause noisy images. The camera housing can be cleaned using normal microscope cleaning material. In case of repair please contact your local Carl Zeiss representation. AxioCam MR Installation + Reference...
  • Page 12 DVD. `çåíÉåíë=çÑ=ÇÉäáîÉêó= AxioCam MR camera head FireWire data cable (6-pin to 6-pin) for power supply to the AxioCam MR and for data transmission between camera and computer DVD-ROM with device driver for AxioVision as well as this Installation+Reference Guide as a PDF file.
  • Page 13 FireWire interface "onboard" When it is being operated on a PC, power is supplied to the AxioCam MR via the 6-pin to 6-pin FireWire cable. On a notebook, a FireWire hub is also required to supply power to the camera.
  • Page 14 PC’s integrated (onboard) FireWire interface In both cases the AxioCam MR is connected to the PC using the FireWire cable (6-pin to 6-pin) supplied with the camera. Power is supplied to the camera through the PC.
  • Page 15 036) also has integrated USB connections. FireWire PCI bus interface card To ensure that power is supplied to the AxioCam MR, no other devices should be connected to the FireWire or USB ports of the FireWire PCI bus interface card.
  • Page 16 To connect the camera to a PC, you require a FireWire cable with a 6-pin connector at both ends. This is supplied with the camera. Connect the FireWire cable of the AxioCam MR to the PCI bus interface card. Connecting the AxioCam MR to the FireWire PCI bus interface card...
  • Page 17 Installation Power is supplied to the AxioCam MR via the FireWire interface card. If you switch off the PC, the camera is also switched off. The AxioCam MR has been designed for continuous operation. During operation the camera may heat up. This is quite safe, and does not in any way impair the functioning of the device.
  • Page 18 PC’s FireWire interface correspond with the power requirements of the AxioCam MR. If you switch off the PC, the AxioCam MR is also switched off. The AxioCam MR has been designed for continuous operation. During operation the camera may heat up.
  • Page 19 Only the basic principles of interface card installation are described in this manual. FireWire PCcard (CardBus) interface card Switch off your notebook and all connected peripherals. Insert the FireWire PCcard (CardBus) interface card into the appropriate slot on the notebook. AxioCam MR Installation + Reference...
  • Page 20 The following components are required: FireWire hub with power supply (order number: 000000-0452-376) 6-pin to 6-pin FireWire cable (supplied with the AxioCam MR) to connect the AxioCam MR to the FireWire hub. A second 6-pin to 6-pin FireWire cable (supplied with the FireWire hub) to connect the FireWire hub to the PCcard (CardBus) interface card.
  • Page 21 The following components are required: FireWire hub with power supply (order number: 000000-0452-376) 6-pin to 6-pin FireWire cable (supplied with the AxioCam MR) to connect the AxioCam MR to the FireWire hub. 4-pin to 6-pin FireWire cable (supplied with the FireWire hub) to connect the FireWire hub to the notebook.
  • Page 22 Installation Connecting the AxioCam MR to the onboard FireWire interface of the notebook The camera is powered by the FireWire hub. The hub must therefore be connected to the power supply. If you switch off the FireWire hub, the camera is also switched off.
  • Page 23 "Resetting the AxioCam MR firmware". As a rule, if the LED is green, this indicates that power is being properly supplied to the AxioCam MR via the data cable. During continuous image acquisition, the color of the LED switches between red (exposure) and green (ready).
  • Page 24 Check the following connections: The AxioCam MR is mounted onto the microscope and is receiving light. The AxioCam MR is connected to the PC or notebook via the FireWire data cable. If you are operating the AxioCam MR on a notebook, the FireWire hub is also connected.
  • Page 25 Installation fåëí~ääáåÖ=íÜÉ=ÇêáîÉê=ëçÑíï~êÉ= In order to operate the AxioCam MR the AxioVision software is needed. First connect the AxioCam MR to your PC (see the section "Setting up the camera system"), and then install the driver software. dÉåÉê~ä= Firstly we would like to emphasize a number of important points: Allow sufficient time for installation.
  • Page 26 Once you have connected the AxioCam MR, the Found New Hardware Wizard dialog appears on your screen. Please ensure that during all the steps below, the DVD-ROM containing the AxioCam MR driver is in your PC’s DVD drive. M 60-3-0014 e / printed 12.2008...
  • Page 27 Installation Select the option Install from a list or specific location (Advanced). Click on Next. Select the option Search removable media floppy, DVD-ROM…). Click Next. AxioCam MR Installation + Reference...
  • Page 28 Installation Under Microsoft Windows XP Professional this dialog window is displayed. Click on Continue Anyway. The last dialog window of the hardware wizard is displayed. Click Finish to close the hardware wizard. To complete the installation follow the steps in the next chapter. M 60-3-0014 e / printed 12.2008...
  • Page 29 In addition to installing the AxioCam MR driver, to carry out full installation of the camera you also need to check and, if necessary, update the camera’s firmware. These tasks are performed by the AxioCam MR installation program, which is described in this section.
  • Page 30 The text window can be closed by selecting this Window's symbol. Set the entry "Cameras and Framegrabbers" - "Carl Zeiss AxioCam" to This feature will be installed on local hard drive. Check the other settings and continue by clicking Next.
  • Page 31 This procedure may take a few minutes. While the firmware is being updated, under no circumstances must the power supply or the data connection to the AxioCam MR be cut off. This would result in the incorrect functioning of the AxioCam MR.
  • Page 32 Double-click the System icon. The System Properties dialog will be displayed. Select the property page Hardware and here the Device Manager button. Now double-click the entry Imaging devices to check the entry Carl Zeiss AxioCam MR. M 60-3-0014 e / printed 12.2008...
  • Page 33 If the entry in the Device Manager must be corrected, i.e. if a question mark or an exclamation mark is in front of the AxioCam MR entry, proceed as follows. Please make sure that during all the steps described below, the DVD- ROM containing the AxioCam MR driver remains inserted in the DVD-ROM drive of your computer.
  • Page 34 Installation The property page General opens. In this case, reinstall the AxioCam MR using the installation program (see section "Installing the camera driver using the setup program"). After the camera driver has been installed and (depending on the operating system you are using) your computer has been restarted, the Device status of the AxioCam MR should be This device is working properly..
  • Page 35 Installation oÉëÉííáåÖ=íÜÉ=^ñáç`~ã=jo=Ñáêãï~êÉ= If the color of the LED on the back of the AxioCam MR does not immediately change from red to green but goes out after the insertion of the FireWire cable, this means that the AxioCam MR’s firmware is not functioning properly.
  • Page 36 "Setting up the camera system". The LED on the back of the camera lights up in red briefly and then goes out. Press the button next to the expansion socket of the AxioCam MR using a pointed object (e.g. a pencil). Keeping the button depressed, briefly remove and then reinsert the FireWire connector on the camera.
  • Page 37 The camera can be mounted onto microscopes with standard TV-adapters with C-mount connections. Carl Zeiss supplies the camera complete with a pre-mounted infrared barrier filter, which offers the optical advantage for use on microscopes of a lower sensitivity to dust.
  • Page 38 OK fã~ÖÉ=^Åèìáëáíáçå= dÉåÉê~ä= The AxioCam MR is a professional, high-resolution digital camera. It has been specially optimized for routine and research applications in the area of light microscopy. This is shown among other by the fast live image, which is displayed on a PC monitor to allow the simple focusing and setting of the sample.
  • Page 39 ^ñáçsáëáçå= If you are using several cameras on your system you must always make the AxioCam MR camera the active camera before proceeding. Start AxioVision by double-clicking on the corresponding symbol. Select from the Acquisition menu the Camera selection ⇒ AxioCam MR3 function.
  • Page 40 Image Acquisition qÜÉ=ïçêâÑäçï=pí~åÇ~êÇ= Live starts and closes the live window. Show live window properties opens and closes the window for adjusting the display characteristic curve and for controlling the camera (exposure time, white balance etc.). Snap acquires an image using the active camera.
  • Page 41 In this drop-down list box you can select the speed of the live image (Slow, Medium, Fast). Click on the icon Live properties to open the live properties. AxioCam MR Installation + Reference...
  • Page 42 Image Acquisition Here you can see the settings for the display of the image like Brightness, Contrast and Gamma. Settings made here are passed on the acquired image. Note: • Only the display is adapted, the camera data remain unchanged. M 60-3-0014 e / printed 12.2008...
  • Page 43 (→ redder) or colder (→ bluer) tones. The Show Channels check box allows you to switch to an alternative setting option if you wish to influence the target value of the white balance manually for each channel. AxioCam MR Installation + Reference...
  • Page 44 Image Acquisition If you are using a color camera, you need to perform a white balance for the image. If you select the automatic balance (Automatic button), the camera tries to determine an optimum value itself. Move the slider to increase or decrease the color intensity of the acquired images.
  • Page 45 You can use this icon to insert a scale bar into your image. The appropriate scaling must have been generated and selected in advance. This icon is used to open the window for generating annotations. AxioCam MR Installation + Reference...
  • Page 46 Image Acquisition Lettering and marking can be inserted in the Draw Annotation(s) window. In the dialog window Draw Annotation(s) the icons scalebar, text, line, rectangle, outline, curve und ellipse are available in the menu line. In the dialog window Draw Annotation(s) a field for Settings for selected items as well as for Font are available.
  • Page 47 If you are using a motorized or encoded microscope, the scalings can be allocated automatically. For further information see Chapt. 9 "Configuration". AxioCam MR Installation + Reference...
  • Page 48 Image Acquisition ^Çàìëí=mêçéÉêíó=m~ÖÉ= This property page contains a summary of the most important camera settings, which are constantly used during operation. M 60-3-0014 e / printed 12.2008...
  • Page 49 The value calculated therefore corresponds to 100% of the camera’s maximum exposure range. The exposure time measurement can also be adjusted to particular lighting conditions. If under certain acquisition conditions the exposure time measurement does not achieve satisfactory exposure of the areas of the AxioCam MR Installation + Reference...
  • Page 50 Image Acquisition image in which you are interested, it is possible to influence the result of this measurement by adjusting the weighting. A setting of 120% means that 120% of the exposure time set in the display window or measured by pressing the appropriate button is used for actual acquisition.
  • Page 51 This setting is optimized for a halogen light temperature at 3200 K, which can be preselected at the touch of a button on many high-quality microscopes. AxioCam MR Installation + Reference...
  • Page 52 Image Acquisition Note: • Setting the white balance to 3200 K generally leads to image reproduction that is closest to the impression of the image in the microscope’s eyepiece, if the microscope has also been adjusted to this value. Note that it is recommended to set the gamma curve for the image display on a value of 0,45 (please find more information in Chapter 2.6 "Practical Notes on Operation in AxioVision"...
  • Page 53 The horizontal axis corresponds to the scale of possible intensity values from dark to light and the vertical axis shows the number of pixels calculated from the current image which possess this intensity value on the x axis. AxioCam MR Installation + Reference...
  • Page 54 Image Acquisition With the color camera the value distribution is displayed separately for each color channel in three lines (red, green and blue). If an image is overexposed, at least one curve on the histogram is cut off at the right-hand edge of the display area, where it forms a maximum. Reduce the exposure time or insert gray density filters into the microscope’s beam path to reduce the amount of light.
  • Page 55 Camera Mode and Frame. `~ãÉê~=ãçÇÉ= RGB and B/W: Two types of AxioCam MR are produced; one with a CCD sensor with a color mask on the chip (AxioCam MRc), and the other with a black and white sensor (AxioCam MRm).
  • Page 56 Image Acquisition With the color variant (AxioCam MRc), you can use these setting options (RGB or B/W) to determine whether the camera should supply a color or a black and white image. This may be desirable for fluorescence images, or to reduce the amount of data.
  • Page 57 Even single-frame exposures produce images with the full basic resolution of the CCD sensor. • The quantity of image data is reduced by a factor of 3 with the same spatial resolution, as no RGB color channels are acquired. AxioCam MR Installation + Reference...
  • Page 58 Image Acquisition _áååáåÖ= The process of Binning ensures that the information in neighboring pixels, in both a horizontal and vertical direction, is summarized on the camera's sensor. This increases image brightness in accordance with the number of pixels summarized. However, this process also reduces the sensor's spatial resolution accordingly. Since the amount of data to be transferred is reduced, the potential image rate is increased.
  • Page 59 Center button. Memory used: Memory used shows the memory size of the acquired image, which depends on the camera resolution, the image size of the selected image frame and of the selected gray value scaling. AxioCam MR Installation + Reference...
  • Page 60 Image Acquisition dÉåÉê~ä=mêçéÉêíó=m~ÖÉ= On this property page you enter the basic settings for the camera. M 60-3-0014 e / printed 12.2008...
  • Page 61 From a technical viewpoint, this technique involves multiplying the data by a corresponding factor. The maximum numerical pixel value generated is always limited to the maximum value of the analog/digital converter you are using (12 bits per pixel per color channel in the case of the AxioCam MR). Note: •...
  • Page 62 Image Acquisition _ä~Åâ=êÉÑÉêÉåÅÉ= Setting a black reference ensures that the image background retains a uniform darkness, even with exposure times in excess of several seconds. This setting is therefore particularly recommended for the acquisition of weak long fluorescence or other images with weak light intensity and consequently exposure times (starting from approx.
  • Page 63 Encoded or motorized microscope stand • Camera belonging to the AxioCam family The following steps are required to set and apply shading correction in the optimum manner: Activate the Automatic check box on the camera property page General. AxioCam MR Installation + Reference...
  • Page 64 Image Acquisition Make sure that all motorized and encoded microscope components are correctly configured in the Micro Toolbox. For the automatic application of shading correction, the correct configuration of the available objectives and the cameras is particularly important (please also refer to the "MTB2004 Configuration"...
  • Page 65 This applies to the following settings in particular: • Lamp adjustment • Köhler setting • Optovar • Camera adapter • Camera port AxioCam MR Installation + Reference...
  • Page 66 Image Acquisition Applying shading correction manually With non-motorized and non-encoded microscopes the automatic shading correction can not be activated. But it is possible to carry out shading correction using a previously generated standard reference image. This image is applied irrespective of the objective set. To generate this file, follow the procedure described above.
  • Page 67 Typical values are between 0.5 and 1.5. 1 = Default. Extended Parameters Further parameters are available. Clicking on the button opens a dialog window, where you can select additional settings. AxioCam MR Installation + Reference...
  • Page 68 Image Acquisition Color Mode This parameter can be switched between RGB = 0 (Default) and Luminance = 1. In RGB mode the Unsharp Masking is calculated individually for each color channel. The color saturation and color of sharpened structures may be changed and color noise may occur.
  • Page 69 This threshold value determines the lower limit from which existing contrast structures are changed. Default: 0 Level High This threshold value prevents existing strong contrasts in the image from being unnecessarily increased any further. Default = 100 AxioCam MR Installation + Reference...
  • Page 70 The meaning of the 9 values, which are separated by a comma, are described above. pÜìííÉê=Åçåíêçä= Via a supplementary cable the AxioCam MR offers a TTL control pulse, which can be used, for example, to control a mechanical shutter (e.g. "Uniblitz") in synchronism with the camera’s exposure time.
  • Page 71 • Shutter closed via AxioVision → than AxioCam MR shutter control. • Shutter open via AxioVision → than AxioCam MR shutter control does not work.
  • Page 72 Image Acquisition cáäíÉê=çéÉê~íáçåë= NIR-Mode The designation "NIR" stands for "Near Infrared". If you activate this mode, it is possible to achieve a further increase of up to 20% in the light sensitivity of the sensor in the range of red and near infrared wavelengths (from approx. 650 nm).
  • Page 73 Gain Analog Gain Frame (ROI) Full frame Image Orientation No changes Black Reference No changes Shading Correction Shutter (Trigger Out) No changes Trigger In NIR Mode No changes Color Saturation Binning 1x1 (sensor basic resolution) AxioCam MR Installation + Reference...
  • Page 74 Close after Snap No changes péÉÉÇ=çÑ=íÜÉ=äáîÉ=áã~ÖÉ= There are three speed modes available for the AxioCam MR live image. If you use the pointer to click on the icon at the bottom edge of the live image, a pop-up menu with the possible setting options appears. The current setting is displayed at the bottom edge of the live image.
  • Page 75 ^ñáçsáëáçå= Below you will find a detailed description of how best to set up AxioVision to achieve optimum color reproduction with the AxioCam MR. Note: • For an optimum color reproduction the monitor first has to be adjusted.
  • Page 76 Image Acquisition With the mouse click on the icon in the footer of the live image. This adjusts the display characteristic curve automatically for an optimum color reproduction of the monitor (gamma = 0.45). In the Properties dialog window, set the gamma characteristic curve in the histogram image on the Display property page.
  • Page 77 A PC graphics card cannot display more than 3 x 8 bits per pixel. However, as we have already mentioned, the AxioCam MR is able to generate 3 x 12 bits per pixel. So that intelligent use can be made of this feature, the display's characteristic curve can be altered in AxioVision.
  • Page 78 Image Acquisition You can now select the area to be displayed by dragging the black rectangles along the characteristic curve or carry out automatic optimization by clicking on the corresponding buttons. A histogram of the gray and color values will be displayed which makes the gray and color distribution visible.
  • Page 79 The output medium has a significant influence on color perception! Use a familiar specimen to adjust the brightness and contrast rendering. If possible also set the color temperature of the monitor to approx. 5000 K or 6500 K. AxioCam MR Installation + Reference...
  • Page 80 Many video cameras have built-in gamma compensation, as they are intended for use on video monitors. iáåÉ~êáíó= All versions of AxioCam MR have been designed to determine linear, quantitative measurement data, as such data is frequently used for tasks in the field of image analysis. Consequently, internal gamma compensation has been deliberately omitted from the AxioCam MR.
  • Page 81 Please also pay attention to all the comments in the file ReadMe.TXT, which is displayed during the driver installation. AxioCam MR does not appear in the menu of selectable cameras Make sure that the AxioCam MR files have been installed in accordance with the installation of the software.
  • Page 82 Trouble Shooting fã~ÖÉ=nì~äáíó= Sudden jolt, vibration or moving objects If the microscope is jolted whilst you are taking a shot, the image will show periodic interference. Repeat the shot and take care to ensure the conditions remain calm. An example of a shaky shot Compare: An error-free image Fluctuations in illumination If the light source has a fluctuating quality of light intensity, stripes or...
  • Page 83 Overlapping exposure and readout of the sensor in fast time lapse images**** Color interpolation High Speed Color- or High Quality Color Mode selectable Hard disk recording Inline recording of image data directly to hard disk at all speeds with AxioVision module Fast Acquisition AxioCam MR Installation + Reference...
  • Page 84 Technical Data Readout of sub frames Freely selectable (ROI) Signal amplification Analog: 2x, digital 32x Digitization 12 bit CCD cooling One stage Peltier cooling Interface FireWire 1394a (400 megabits/s) Range of integration 1 ms up to 60 s time Signal output 2 x TTL-Out: exposure time and readout time (i.e.
  • Page 85 Overlapping exposure and readout of the sensor in fast time lapse images*** Hard disk recording Inline recording of image data directly to hard disk at all speeds with AxioVision module Fast Acquisition Readout of sub frames Freely selectable (ROI) AxioCam MR Installation + Reference...
  • Page 86 Technical Data Signal amplification Analog: 2 x, digital 32 x Digitization 12 bit CCD cooling One stage Peltier cooling Interface FireWire 1394a (400 megabits/s) Range of integration 1 ms up to 60 s time Signal output 2 x TTL-Out: exposure time, readout time (i.e. for driving connectors external electric shutters), 1 x Trigger-In to start an acquisition...
  • Page 87 The AxioCam MRm (black/white version) is used without infrared barrier filter. If necessary, an additional infrared barrier filter can be inserted between the microscope adapter and the camera. AxioCam MR Installation + Reference...
  • Page 88 14, 15 image orientation 55 connecting to the PC 10, 11 image properties 71 contents of delivery 6 image quality 76 contrast, change 72 infra-red barrier filter 31 control signal 65 AxioCam MR Installation + Reference...
  • Page 89 Index installing the camera driver using the scaling histogram 48 setup program 23 seting up the camera 5 installing the camera driver with the settings 42 hardware wizard 20 setup program 23 installing the driver software 19 shutter control 64 software problems? 75 spectral sensitivity 81 speed modes 68...