ZEN 2012 - Service Pack 2 (blue edition)

– Readme –
© Copyright 1999 – 2013 by Carl Zeiss
This document provides important information about known bugs in ZEN 2012 SP2 (blue edition)
and describes workarounds if available.

Acquisition – Experiment Designer

57529
Frequent annotations for ‘carrier container name’ displays the incorrect value when used in multi-
block experiments.
Workaround: using the function ‘1 separate image document/ acquisition block’ that can be
activated in the experiment designer tool.
65517
Zoom levels of Axio Zoom.V16 are not correctly stored in experiments consisting of multiple ‘blocks’
(created with Experiment Designer). This may lead to incorrect analysis- display- oder processing-
results of functions that require this information.
65518
When running Multiblock experiments (Experiment Designer) the XY scaling is set to ‘pixels’ for all
blocks but block 1. This happens with the Split blocks into individual files option.
Workaround: manually editing the pixel values for the ind. block images.

Acquisition – Fast Acquisition

65768
Experiment files created on a system equipped with Fast Acquisition hardware for for running
experiments in a triggered manner should not be used on systems without this type of hardware.
Doing so can cause a time out error that prevents the experiment from been excuted correctly.

Acquisition – Focussing
58136
The image update is very poor when running a software autofocus.
66088
The Definite Focus can become inoperable under the following condition: If used for a Time Series
experiment and the interval between time points is very short (e.g. smaller than 1 sec) enabling the
periodic stabilization of the Definite Focus (e.g. with an interval of 10 sec) can cause problems.
Workaround: using the focus configuration in the Time Series Loop on the Focus Strategy tool
window, e.g. ‘Run Definite Focus every 10th Time Point’.

Acquisition – General Acquisition Aspects

66310
If both All channels (global) and channel specific shading corrections are created on the acquisition
tab the results are not as expected.
The situation is as follows:
- when working from acquisition in order to use shading correction the Shading Correction checkbox
in the Channels tool always has to be selected.
- Defining an All channels shading correction (Acquisition mode/Prost Processing/Shading
Correction/All channels) works without problems
- Defining a Channel specific shading correction (Acquisition mode/Prost Processing/Shading
Correction/Channel specific) also works w/o problems
- the problem arises when selecting a channel, defining a All channels shading correction in the
Acquisition mode tool, selecting a second channel and performing a Channel specific correction

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© Copyright 1999 – 2013 by Carl Zeiss
 only the All channels correction will be used. This means, that one cannot combine both methods in
one experiment.
Solution:
If a Channel specific correction shall be used, defining only a Channel specific correction for all
channels will work.
If an All channels correction has already been made, deleting it in the calibration manager
(Tools/Calibration Manager/Shading References) will solve the problem
If a global shading correction shall be used, deleting all calibrations in the calibration manager and
creating a All channels calibration will also solve the problem.

Acquisition – Smart Setup

54549
Reflected light shutter mistakenly set to open in TIRF systems configurated with a HXP lamp and
reflected light shutter of the microscope. A Workaround exsists and the settings can be corrected by
hand.
65505
When setting up a bleaching experiment Smart Setup does not use the Beamcombiner reflector
position.

Acquisition – Tiles and Positions

60061
Frequent annotations for ‘carrier container name’ displays the incorrect value when used in multi-
block experiments.
Workaround: using the function ‘1 separate image document/ acquisition block’ that can be
activated in the experiment designer tool.
65330
In the current implementation, the display update of a large tile region during acquisition will be
performed in a block wise manner leading to visual artifacts.
However, after acquisition everything is displayed normally.
65511
Scene naming (ID) is incorrectly displayed in ZEN Tree view for satellite image files created when Tiles
option ‘split scene into separate files’ is used.
This is a ZEN display problem only - the metadata is correct.
Work-around is, to use the post acquisition function ‘Split scene (write files)’ from the Processing tab
as an alternative to the option ‘Split scenes into separate files’ on the Tiles tool in Acquisition tab.
65667
When working with a carrier with multiple containers the check box ‘Move Focus Drive to Load
Position Between Container’ applies only to the experiment.
This function is ignored when working interactively with the sample, for example when manually re-
checking tile regions/positions in different containers!
65917
It is not possible to modify a drawn tile region because it is below the blue Live navigator frame.
Workaround: delete the grid and redraw again to the desired size or move the Live navigator frame
to a different location.
65938
The calibration state of the stage in Locate tab is not transfered to the Sample carrier calibration
dialogue of the Tiles tool in the Acquisition tab

Acquisition – Timelapse
61907
The Axiocam 605 color/mono camera can deliver imaging date with a speed of 240 MBytes/s.

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It is possible that the data handling capacity of certain PC systems can be exceeded when running the
camera in a fast time lapse or movie recorder application.
The results can be dropped frames.
As a default, any acquisition will be aborted in such a case to prevent inconsistent imaging data.
Therefore it is recommended to use fast CPUs, large main memory setups and fast hard drives in
order to avoid this situation.
Other option:
If dropped frames can be accepted, it is possible to suppress the stop of the acquisition by
deactivating the detection of missed frames:
go to the menue Tools - Options - Acquisition: activate ‘Show Camera Expert Options’.
Two relevant functions will be shown in the camera dialog ‘Model Specific’:
- deactivate ‘Abort on missed frames’. The Movie recorder keeps on recording images, even the
dropped frame event occurs,
- enter a ‘Frame Time’ larger than zero. The Frame Time parameter slows down the acquisition
speed of the camera at short exposure times or at selected small sensor sub frames (ROIs).

Analysis – Advanced Automated Analysis

61271
If you acquire an image via image = Zen.Acquisition.Execute(ExperimentSetting) and rename it with
image.Name = NewName the GUI of ZEN will not show the new image name but displays the original
(old) name.

Analysis – Analysis
65704
Contours which are drawn in the Interactive Segmentation step of the Image Analysis Wizard may get
lost when the drawing of the contour is finished with double-click with the right mouse button.

Analysis – Colocalization
65594
Colocalisation does not work with multiscene images.
65744
Colocalization cannot be done directly on images with multiple scenes. The Coloc view is not
available.
Workaround: use the Split scenes function (Processing/Utilities/Split scenes) to create one file per
scene which makes the Coloc view available.

Analysis – Physiology
65521
Relates to the current feature set. MeanROI view can not yet deal with multi-block experiements.
Workaround is a separation of the block and individual analysis.
65790
The streaming mode cameras prevents the use of certain functions in ZEN: for example Physiology
experiements are incompatible with streaming mode as this speacial acquisition mode does not
allow the appropraite measurements to be made. Currently no warning message or infomation text
is displayed to this effect.

Axioscan
66120
If the user opens the Scan Profile Wizard the software will populate the dropdown selections for the
the Tray and slides and match this with the current content of the magazine. If you insert or remove
trays while the wizard is open these changes will not be updated in the dropdown menus for the

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© Copyright 1999 – 2013 by Carl Zeiss
tray/slide selection. This can be avoided by making sure to insert the needed trays/slides before
activating the Scan Profile Wizard.

Devices – ApoTome
65808
Some of the histogram tools in the ApoTome calibration wizards are not visible when in the ZEN Light
style.
Workaound: switching to Dark style
65834
When crerating focus calibrations for the Axiozoom.Z1 for the 4 click stop positions the status in the
wizard still states not calibrated. The calibrations are, however, correctly done and all experiments
can be performed.
65835
When in step 5 of the phase calibration wizard the buttons for ‘Full-Scan’ and ‘Local-Scan’ appear to
be inactive.
Workaround: please click into the buttons to make them active.
66248
The first time after ZEN installation when the focus or phase calibration wizards are started the live
image performance is very poor.
Solution: restarting all components (PC, microscope, ApoTome etc.) after which the live image
performance will be as expected.

Devices – Cameras
60653
In some rare cases hot pixels are not completely removed by the Black Reference correction.
These pixels show a nonlinear behaviour and can not be removed with the available algorithm.
However they can be removed effectively by the Noise Filter function in the camera menue section
Postprocessing.
61013
The Photometrics Myo camera cannot be used in ZEN when running from internal USB 3.0 ports.
Workaround: using a separate USB card such as Exys EX 11094. Please follow the manufacturers
recommendations.
61016
With the Photometrics Myo camera when running from internal USB ports the following problem
exists: SNAP cannot be used while running the Live image.
Workaround: This is due to a bandwidth problem, using a separate USB card such as Exys EX 11094
might solve this problem.
61615
For the Axiocam 105 color, performing AutoFocus while Spot Meter is activated takes more time
than performing AutoFocus with Spot Meter deactivated. Workaround: Use the following Software
Autofocus settings: Quality = Basic; Range Coverage = Smart.
63910
On PC's where an interface board for an older model AxioCam was installed once but has been
removed ZEN starts with an error message trying to initialize the non existing camera.
Solution: manually removing ‘mcam64.dll’ from C:/Windows/System32.
65298
For the AxioCam ERc 5s, when an ROI is set, it assumes that the Image Orientation is always set to
Original. If the user sets an Image Orientation besides Original, this can result in the ROI portraying
an undesired region.
65300
Shading Correction is not correct when the Axiocam 105 color is set to 2x2 or 4x4 Binning.

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© Copyright 1999 – 2013 by Carl Zeiss
65328
For the AxioCam ERc 5s, White Balance can only be properly achieved in restricted lighting/exposure
conditions. Generally, bright situations are more likely to allow a proper White Balance. The
exposure time will vary between different White Balance settings.
65530
AxioCam Erc5s: When Bad Pixel Detection was not successful, the LED is flashing. Workaround:
unplug and replug the camera.
65531
Setting the Saturation may cause color shifts.
65586
Stressing the system by pressing camera GUI buttons randomly in a quick sequence can produce
spurious images (empty or wrong content).
65588
Modifying the microscope configuration while the Live image is active in some cases freezes the live
image.
Workaround: It has to be closed and reopened to become live again.
65593
The Set Exposure button in the Action button bar does not show a warning message when the light
intensity is too high to be adjusted correctly by exposure measurement.
66043
The maximum frame rate achievable with the Hamamatsu Orca Flash 4.0 in ZEN is ~80 frames per
second. This is due to performance limitations of the PC as well as the acquisition engine of ZEN.
66313
Axiocam 105 color: The current Exposure Time range is 31 microseconds to 2.6 seconds. The range is
supposed to be 100 microseconds to 2 seconds.

Devices – Dual Camera

60890
The live image speed for dual camera is reduced to not more than 8 frames per seconds compared to
a live image of a single camera. This is to avoid technical problems when running two cameras
simultaneously.
65569
Both calibration routines for DualCamera do not work correctly in combination with acquisition ROIs.
65570
DualCamera: Different LiveSpeed <->Binning does not work in combination with calibration
65655
Repeatedly changing the binning in the acquisition mode tool for dual camera experiments leads to a
wrong behavior of the ‘use dual camera calibration’ checkbox. Since calibrations need to be done for
every binning and camera ROI changing to binning without a valid calibration might result in
uncalibrated dual camera images while the check box suggests otherwise.
Workaround: defining the desired binning only once will prevent this problem.
65775
Running a software autofocus on SD system equipped with a dual camera has the following bug: Both
lasers from each track will be switched on for the SWAF run despite that fact that only the laser
associated with the reference channel in the channels tool should be used.

Devices – Microscopes and Stages

61614
ZEN Lite only supports fully manual stands. If a manual Axio Imager.A1/2 is configured in the MTB
2011 configuration program which contains a lamp switch, the microscope is not displayed in the
light path.

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© Copyright 1999 – 2013 by Carl Zeiss
Workaround: configuring an ‘Other’ stand instead.
65506
When resetting the XYZ Positions to zero on the microscope TFT control the new changed
coordinates are not transferred to the software. This can lead to potentially erroneous movements of
stage or focus if the experimental parameters such as tile or focus positions are different.
Workaround: restarting ZEN after resetting the position values in the TFT or redefining tiles, positions
or focus in the experiment.
65633
Axio Zoom.V16: motorized stage moves slow when controlled through the software joystick.
Operation during acquisition is not affected.
Workaround: moving the stage via the hardware joystick
65827
When setting XY position or Focus position to zero on the TFT of the microscope ZEN still uses the old
values.
It is very important therefore to NOT set the TFT positions to Zero while ZEN is connected to the
microscope as running experiments with prestored positions might cause damage to sample or
objective.
65383
The Transmitted Light On/Off button on the locate tab does not follow the switching state of the
Halogen lamp correctly. This only happens if no shutter is present in the microscope.
65940
Manual photo tube with motorized shutter shows up as 30/70% only irrespective of the true split
ratio.

Files and Data – Data handling

65332
When using the Save all function to save a series of images acquired from the acquisition tab, the
images will be saved correctly at the designated folder location but the temporary files stored in the
Temp directory will not be deleted. Also, the images will still be marked as unsaved with the star
symbol.
Workaround: Instead of Save all use the standard Save function for each image.
65596
It is possible to have 2 active File Browser documents. With such a setup, the tree views and view
control Tools tabs are not synchronized, but the corresponding table- and gallery views are. Display
refresh and sorting will not work properly.
65690
Mirax images when loaded show a black background in areas without tiles.
No known Workaround.
65738
Result image of OME-TIFF-Export will have wrong values concerning the depth of focus.
65806
Loading large images from remote network locations can take a long time without progress
indication. Clicking into the application window during that phase might result in a ‘ZEN is not
responding’ message. After the full image has been loaded the application becomes responsive
again.
66046
When importing an OME-TIFF file the time information may get lost and/or bit depth may be reduced
to 8 bit.

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© Copyright 1999 – 2013 by Carl Zeiss
Files and Data – Import and Export
57978
Export for Mulitblock images only works for the first block. This is true for either interactive or batch
export.
Woraround: Using the new processing function ‘Split Multiblock Image’ it is possible to separate all
blocks and fuse them together to create one new image document per block. Since these are
homogeneous they can then be exported as usual.
58050
A corrupted file will remain on the disk, if the disk space is not sufficient for the saved or exported
image.
65509
The process of ZVI-Export could not be stopped by Cancel or Abort.
65644
Image annotations in AxioVision ZVI images are not always shown correctly when opening them in
ZEN.
Workaround: redrawing them in ZEN.
65656
Image imported with Image Import has always a normalized display curve.
65673
ImageExport does not make a difference if checkbox 'Convert to 8bit' is activated/deactivated for
'Apply display curve and channel colors'.
65741
Imported tiles (image import function), generated with ImageExport using retiling option, will have
different image size than original image.
65742
Import of a few parts of images can result in an offset between a few parts.

General – Display Settings

57438
Clicking Min/Max or Best Fit for tiled images with pyramid levels do not produce the expected display
settings leading to dark display. The reason is, that areas without image data are calculated as 16 bit
white areas which then are included in the calculation.
Workaround: clicking on Reset to reset the display curve to the camera bit depth and manually
adjusting the display curve.
65626
Lambda-stacks do not have a tinting-color
65746
Display histogram update during an experiment with Min/Max or Best Fit is limited to image display
sizes <2000 x 2000 pixels. Hence large (Tile) image histograms have to be adjusted via the lower and
upper range grab bars at the left and right hand edges of the histogram area.

General – Graphical Elements

53159
Closing the Format graphical elements dialog with ESC does not work until something in the dialog is
highlighted.
65515
Copying and pasting graphical elements from one scene to another scene of a multiscene image
pastes the element into the original scene instead of the chosen one.
Workaround: split scenes using the split scenes function (Processing/Utilities) first.

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© Copyright 1999 – 2013 by Carl Zeiss
65747
Resizing graphical elements becomes impossible, if they are lying above another graphical element.
The resize handles are shown but instead of resizing the active graphical element the one below is
being moved.
Workaround: Locking the element below (lock symbol in the Graphics view options tab) before
resizing.
65752
Frequent annotations drawn into very large images such as created by Axioscan cannot be read
because they are too small.
Workaround: creating custom annotations with the proper font size and disabled Zoom with image
option.
65753
The graphical element type ‘Events’ is not visible when drawn into very large images (e.g. Axioscan).
Workaround: defining an event tool in the custom toolbar with the property Zoom with Image turned
on.
65760
Merging a ‘Contour with Holes’ with another graphical element the holes are not present in the new
element anymore.
No known Workaround.
65761
Merging two Spline contour graphical elements the resulting element becomes a polygon contour.
No known Workaround.
65763
Merging complex graphical elements sometimes results in wrong results such as several elements
instead of one.
No known Workaround.
65779
Adding a text annotation to a very small text box makes the text disappear after typing.
Workaround: Selecting the text box element in the Graphics view options table and resizing it so that
it can fit the text.
66160
Some annotations such as relative or absolute focus position are not shown correctly for processed
ApoTome images if the image has been acquired using the Experiment designer (Multiblock)

General – GUI Basics

60183
When opening images created with ZEN Black (*.lsm or *.czi) the units displayed in the image ruler
are in nanometer while the infoview shows the correct µm unit.
65552
If another window is open (e.g. Diagnostics, Kitchen Timer,...) and it will be closed, the application
will send to Background if another application was activated (ALT+TAB keys and task bar).
65557
Not all shortcuts work as specified or are not implemented.
65758
Graphical elements when put onto the microscope TFT control as softkeys produces error messages.
No known Workaround.
65769
The sliders for some microscope components do not work correctly: the ghost slider which should
show the actual position of the device shows erratic movement. However, the device operation itself
is ok.

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© Copyright 1999 – 2013 by Carl Zeiss
65795
The following dimensions cannot be played when in Full Screen (F11) mode: Blocks, Scenes, Phases
(ApoTome)
65836
The time stamp shown in the picker tool deviates slightly from the frequent annotation time stamp.
This is due to a rounding error. The frequent annotation acquisition time is the correct value.
65922
If an image is saved to a removable drive, and the drive is removed before the image is closed, the
program enters an infinite error dialog loop when closing unless the drive is reattached.

General – XY Scaling
65426
Different Magnifications within a heterogeneous experiment are not updated in the file data.

General – ZIS Lite

65657
When a camera is not licensed (or the dongle is not present), the Snap and Live button are still
accessible.
When presssing them, an error message appears. The Snap and Live button should be grayed out in
this case.

OAD – OAD - Framework

58114
ZEN is written in WPF and large strings (~Gigabyte) causes WPF to crash. This situation may occur e.g.
when a large integer is multiplied with a string.
60182
Functions registered with the exit handler (atexit) are not called at the end of the macro. They are
called after pressing the Reset button.
66115
Zen does not respond in some cases during macro execution.
66116
Generating a ZenImage with ZenPixelType.Bgr192ComplexFloat may cause an error.

OAD – Scripting-IDE
61307
In some rare cases an error appears if macro has empty lines in combination with for-loops or the if-
statement. Usually closing and opening the macro editor repairs the error.
61432
Sometimes the macro editor shows the error message with a wrong line number, e.g. TypeError:
unsupported operand type(s) for /: 'str' and 'int' in line -1
62919
Sometimes the Debugging Pointer stops or remains in for loops with more than one nesting level.
63944
In some rare cases an error appears if macro has empty lines in combination with for-loops or the if-
statement. Usually closing and opening the macro editor repairs the error.
66077
Calling a macro via toolbar button changes the file in the macro editor.

OAD – Simple interface

58261
The function Zen.Processing.Transformation.Geometric.OrthoView(..) supports only the
ZenProjectionMethod Average and Maximum.
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© Copyright 1999 – 2013 by Carl Zeiss
60996
Set exposure button in camera tool is not recorded. Please use Exposure button on locate tab.
60997
If the last bracket of a function is not closed in a macro. the macro environment slows down
significantly. Usually closing and opening the macro editor allows to go on working with the macro.
61415
Some Image Processing Functions are not recorded. You will get a message as a python comment like
'#Could not record function '...' . The function is not available in Simple Interface or has a different
name.'
63527
In the processing functions Addition, Substraction etc. the enum ZenAdditionMode.Absolute is not
available for the python macro.
65413
The interactive threshold slider function has an update problem when used within a macro. The
sliders have to be used a second time to update the user interface.
65440
The title of the image shown in the center screen area is not updated, when using a macro to rename
the image.
65767
An error message appears, if an expereiment is executed and the Locate Tab is active.
To avoid this error switch first to the Acquisition Tab.
66059
Deleting an experiment in a macro causes a popup dialog which must be confirmed.
66118
Exported files may not be saved in the selected folder, when using ImageExport in a macro.

Processing – Image Processing - general

52368
The tile stitching function with the New Output and Fuse option active might take very long for large
tile images.
58168
Working with the Denoise Function on large images may cause the computer to be inaccessible.
65516
32bit floating point images cannot be exported to TIFF correctly, the resulting image is a 24 bit rgb
TIFF.
No known Workaround.
65599
Image Processing: Image calculator requires second parameter although not used.
65606
When burning in graphical elements using the Burn in annotations function the font size in the result
is different from the original if the ‘Zoom with Iimage’ property is not set.
Workaround: Turning on ‘Zoom with image’ and defining the desired font size.
65653
Applying the Resample IP function causes a loss of associate time stamp information for time series
data sets in the resulting output image.
65654
Some processing function parameters are needlessly changed when loading a new input document.
This can lead to unexpected results.
Workaround: Clicking on the Default button in the parameters tool or manually correcting the
parameters.

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65701
The preview function for some processing functions is very slow for large Axioscan images because
the calculation is done on the highes reSolution only.
65764
Performing the image processing function Auto Threshold on very large 2D images takes very long
time. This operation cannot be stopped.
No known Workaround.
65830
When using the processing function Rotate the output image does not preserve the original relative
time annotation.
66297
Multiblock images show numerous problems for most image processing functions.
Solution: using the new Split Multiblock Image function to create separate homogeneous images for
each block. These images can be processed as usual.

Reporting – Reports
65978
Reporting - Report Preview - When several images are dropped into the report and the template is
changed, only the active image stays in the report.

Views
61523
Copying and Pasting display settings from and to multiblock images fails for all subsequent blocks.
Workaround: manually defining and applying the desired display settings to a multiblock image.
65229
When playing through a time series or a z-stack while in Split view the image updated sometimes
lags. As a result the image display shows brief gray flickering in between image updated. This
behavior improves once each image in the series has been shown once.

Views – 2.5D View

65551
When in 2.5D view, there is limited travel range for viewing. If there is no change in the zoom or
angle (home position), the top of the rendering is cut off by the container frame.
65793
12 Bit images are displayed as 16 bit in 2.5D View.

Views – 2D View
65729
The ruler in the image display (Tools/Options/Documents/Show Rulers) shows pixel values instead of
scaled units during acquisition. After the experiment is finished, the correct units are shown.
65734
When switching to OrthoView during acquisition of a z-stack, the view is switched back to 2D view
upon experiment completion.
65735
Switching between image documents resets the layout of the view options tabs in the center screen
area, involuntarily discarding user changes to the tab layout.
66004
Cameras which can acquire images faster than the live image rate possible sometimes show artifacts
in the Live image when looking at fast moving objects. This does not affect the acquisition
performance.

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© Copyright 1999 – 2013 by Carl Zeiss
66161
Under the following condition the dimension tab shows a wrong behavior:
- ApoTome multiblock images with a brightfield channel as first channel
- switching to single channel mode in Dimensions
- selecting one of the fluorescent channels
- moving the z-slider will provoke calculation of the sectioned image
Result: after the calculation is finished, the display jumps back to the brightfield channel
Workaround: Creating a processed image by clicking on the Create button in the ApoTome view
options tab before playing through Z.

Views – 3D View
65504
3D View: Rendering of Time series is not possible with 3D textures
65545
Under certain circumstances the cutting planes cannot be moved by mouse.
Workaround: moving the planes by slider.
65549
Intersections of two or more clipping planes aren't shown as lines.
Workaround: choosing the Colored option in Clipping view options tab.
65550
Inner surface lighting sometimes does not work when the Color Inner Surfaces option is activated.
No Workaround available
65662
The 3D rendering window is controlled via the mousewheel even if another program is active in the
foreground.
Workaround: switching to 2D View before operating the mousewheel in the other program.
66008
Switching Bachground-color is not longer possible in Maximum-3D-View when in GPU rendering
mode. Even selecting a white background in any other view-mode and selecting Maximum-Mode
afterwards will make the backgroundcolor switch to black.

Views – Info View

65450
The tracks table in Info View constantly changes the column width when looking at Multiblock
images.
65666
The entries of the fields FILTER, Laser Blanking and Beamsplitter are often empty for .lsm-images.

Views – Splitter Document

65739
Multiblock images do not work well in Splitter mode, the display settings are not correctly applied
and sometimes a gray area is shown instead of images.
Workaround: using the image processing function Time Stitching and creating a homogeneous
version of the multiblock image. These can be compared within splitter documents.

Views – Tree View

61364
In some cases, the treeview shows the Depth of Focus for the first channel only, although the other
channels have correct values in other views.

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© Copyright 1999 – 2013 by Carl Zeiss