Carl Zeiss ZEN 2012 (blue edition) ReadMe

(c) Copyright Carl Zeiss Microscopy, March 2013 This document provides important information about known bugs in ZEN 2012 SP1 (blue edition) and describes workarounds if available.

2.5D View (Views)

21787 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.

2D View (Views)
41149 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. 41253 When switching to OrthoView during acquisition of a z-stack, the view is switched back to 2D view upon experiment completion. 41254 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. 43177 The view port scalebar available for large tile images jumps around when changing the software layout (full screen, closing or opening right tool area etc.)

3D View (Views)
21441 Under certain circumstances the cutting planes cannot be moved by mouse. Workaround: moving the planes by slider. 21715 Intersections of two or more clipping planes aren't shown as lines. Workaround: choosing the Colored option in Clipping view options tab. 21719 Inner surface lighting sometimes does not work when the Color Inner Surfaces option is activated. No workaround available 27086 3D View: Rendering of Time series is not possible with 3D textures 33179 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.

Analysis (Analysis)
35786 Batch processing is not able to compile measurement data into a single table. Only known workaround: performing the measurement using the macro environment. 39487 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. ZEN 2012 SP1 (blue edition) Readme, March 2013 Page 1

ApoTome (Devices)
37028 The Auto Exposure checkbox in the second step of the grid focus calibration wizard does not work properly, the exposure times fluctuate strongly. Workaround: uncheck autoexposure and using manual exposure control. 40240 Occasionally during phase calibration an error appears reporting a wrong wobble position of the Grid. Sometimes this can lead to a non-reacting ApoTome slider. This is due to a firmware bug, the controller needs to be updated accordingly. 41068 When combining ApoTome with Tiles the image display during acquisition only shows the first phase (=grid) image. This is due to timing issues which make online ApoTome processing impossible. However, after acquisition has finished, the ApoTome processing takes place and the ApoTome display options tab is available. 43437 When acquiring inhomogeneous ApoTome images using the Experiment Designer function the resulting multi block ApoTome images show wrong display behavior when jumping between blocks. Workaround: Acquiring multiblock images as separate files. 43909 When using Display functions BestFit or Min/Max on inhomogeneous multi block ApoTome images the block slider jumps back one block. Workaround: closing the right tool area prevents that problem from occuring.

Cameras (Devices)
19785 AxioCam Erc5s: When "Bad Pixel Detection" was not successful, the LED is flashing. Workaround: unplug and replug the camera. 19804 Setting the Saturation may cause color shifts. 24150 Stressing the system by pressing camera GUI buttons randomly in a quick sequence can produce spurious images (empty or wrong content). 24615 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. 25941 When starting ZEN for the first time the white balance is set to 1,1,1 instead of setting it to the values for 3200 K. 42343 When operating the AxioCam HRc/m in High Accuracy Mode at exposure times shorter than 1,8 ms communication errors between camera and computer can occur. Please use longer exposure times and reduce light intensity, or switch to High Speed Mode. The camera modes can be selected under the Menue section "Camera Specific" --> Readout Speed 43781 With the AxioCam HRc/m camera operated in the High Accuracy (14 bit, 12.5 MHz) mode in some circumstances two images are acquired internally before acquiring the final image. This can cause unexpectedly long acquisition delays. Workaround: setting the camera to high speed mode (Camera/Camera specific/Readout mode). This behavior does not influence experiments run from the acquisition tab, however. ZEN 2012 SP1 (blue edition) Readme, March 2013 Page 2

Colocalization (Analysis)
24721 Colocalisation does not work with multiscene images. 42308 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.

CorrMic - General aspects (Acquisition)

43428 Description: Resolution is limited to 1024 x 768 for Shuttle and Find in ZEN SEM 2012 for EVO, Sigma, Ultra, Supra, Auriga and Auriga Compact running under SmartSEM 5.5. Workaround: Do not change the resolution, otherwise a restart of the EMServer and SmartSEM is necessary after these processes are closed using the task manager.

Data handling (Files and Data)

25578 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. 37784 A corrupted file will remain on the disk, if the disk space is not sufficient for the saved or exported image. 38633 Mirax images when loaded show a black background in areas without tiles. No known workaround. 39245 Scene naming (ID) 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. 41536 Result image of OME-TIFF-Export will have wrong values concerning the depth of focus.

Display Settings (General)

27093 Lambda-stacks do not have a tinting-color 42393 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.

Dual Camera (Devices)

23421 Both calibration routines for DualCamera do not work correctly in combination with acquisition ROIs. 23422 DualCamera: Different LiveSpeed <->Binning does not work in combination with calibration 31608

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Dual Camera calibration can not be enabled. Reason is, that the hardware state of light sources or filters which is being used during calibration is not active outside of a running experiment. Workaround: Ignoring the error message, because the experiment is being executed with a correct calibration. 43547 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.

Experiment Designer (Acquisition)

43524 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 processingresults of functions that require this information.

Fast Acquisition (Acquisition)

43341 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. 43713 If a Time Series or Z-Stack experiment is run in triggered or compromised mode, the stage position is always recorded as 0,0. This can be seen, for example, in the Info View. It works correctly in interactive mode or if Tiles is added as an experiment dimension. 43857 When using the lightsource Sutter DG4 in triggered mode and doing multichannel z-stack using software autofocus at the same time the light source control gets out of sync with image acquisition leading to wrong images. Three workarounds exist: 1) Using the all channels per slice option only; 2) not using the software autofocus in triggered mode; 3) setting up a multiblock experiment (Experiment designer) with the autofocus running in a interactive mode experiment block.

File format (Files and Data)

20614 The display range of the live image histogram is not automatically updated if the camera bit depth is modified while live is active (all Evolve models). 21371 Different Magnifications within a heterogeneous experiment are not updated in the file data.

Focussing (Acquisition)
31884 ZEN does not support a standalone Piezo-Z-drive for microscope stands that do not generally support motorized z-drives. 43444 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".

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Gallery View (Views)

17045 The Create image function in the Gallery view options tab creates an image which does not show the annotations present in the original document. Workaround: adding annotations by drawing into the created image document.

General Acquisition Aspects (Acquisition)

28616 Due to technical reasons in the camera hardware it is not possible to adjust the frames of an region of interest with pixel precision. Both the offset and the size values may be restricted to certain values and step size. 43845 The Option "Automatic Mode" is only valid for the Locate Tab, where this works - a new snap overwrites the existing image document. It does not have any affect on the SNAP functionality for the Acquisition Tab, where always a new Snap will be created.

Graphical Elements (General)

27620 When drawing a scale bar into a image using the Continuous mode and changing the objective, the scale bar is redrawn but not positioned correctly. Workaround: redrawing the scalebar for the new resolution. 28034 Saving graphical elements also considers stage coordinates when acquisition was done with a motorized stage. Loading such files on images with other stage coordinates positions the graphical elements according to their stored corrdinates and not relative to the new image. Workaround: Using Copy/Paste to copy graphical elements from one to another image 31574 The format graphical elements dialog assumes the wrong size when previously opend for the graphical element of the type "grid". Workaround: Closing and reopening the image and opening the format dialog for any graphical element other than the "grid" tool first. 35477 Using the Reset function in the format graphical elements dialog does not reset the color of the icon in the list of graphical elements on the Graphic view options tab. The color of the graphical element itself is reset however. Workaround: redrawing the graphical element. 42400 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. 42982 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. 42983 The graphical element type "Events" is not visible when drawn into very large images (e.g. Axioscan). ZEN 2012 SP1 (blue edition) Readme, March 2013 Page 5

Workaround: defining an event tool in the custom toolbar with the property Zoom with Image turned on. 43110 Merging a "Contour with Holes" with another graphical element the holes are not present in the new element anymore. No known workaround. 43111 Merging two Spline contour graphical elements the resulting element becomes a polygon contour. No known workaround. 43114 Merging complex graphical elements sometimes results in wrong results such as several elements instead of one. No known workaround. 43611 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. 43735 When changing the text position of graphical elements and saving into non-CZI fileformats such as JPEG upon reopening the image all text is drawn into the top left corner of the image. Workaround: not moving the text. 43789 Choosing measurement features for graphical elements via the context menu entry is not possible for images which reside in a second or third view container. In some cases the choose measurement features option remains grayed out for the rest of the session. Workaround: changing measurement parameters for a graphical element tool beforehand in the custom toolbar or moving the image to the first container.

GUI Basics (General)

21821 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). 40547 Working with two monitors of different size can cause problems when maximizing the ZEN application. 43085 Graphical elements when put onto the microscope TFT control as softkeys produces error messages. No known workaround. 43384 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. 43815 When starting ZEN a white screen briefly appears which might be disturbing in dark environments. Unfortunately, no workaround is known.

Image Processing - General (Processing)

25654 Image Processing: Image calculator requires second parameter although not used. ZEN 2012 SP1 (blue edition) Readme, March 2013 Page 6

25986 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. 29928 Applying the Resample IP function causes a loss of associate time stamp information for time series data sets in the resulting output image. 31003 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. 39367 The preview function for some processing functions is very slow for large Axioscan images because the calculation is done on the highes resolution only. 43136 Performing the image processing function Auto Threshold on very large 2D images takes very long time. This operation cannot be stopped. No known workaround. 43450 32bit floating point images cannot be exported to TIFF correctly, the resulting image is a 24 bit rgb TIFF. No known workaround. 43866 The naming option for the Split Scenes (Write files) function does not work if the orignal file name contains period's (e.g. "01.12.2012_Filename.czi"). Only the first scene is actually written to disk. Workaround: Renaming the file name to avoid period characters.

Import and Export (Files and Data)

28515 Image annotations in AxioVision ZVI images are not always shown correctly when opening them in ZEN. Workaround: redrawing them in ZEN. 37693 The process of ZVI-Export could not be stopped by Cancel or Abort. 39541 Exported tile images show the overlap of the neighbor tiles, if apply display curve and channel colors is activated in the ImageExport function. 41054 ZVI-Export of CZI-ApoTome images does not work and gives error messages. 41653 Reloading of exported retiled OME-Tiff images can result in a system crash. 36793 ImageExport does not make a difference if checkbox 'Convert to 8bit' is activated/deactivated for 'Apply display curve and channel colors'. 32438 Image imported with Image Import has always a normalized display curve. 41707 ZEN 2012 SP1 (blue edition) Readme, March 2013 Page 7

Imported tiles (image import function), generated with ImageExport using retiling option, will have different image size than original image. 41710 Import of a few parts of images can result in an offset between a few parts. 30720 Image Import: Reload function does not appear, if file list is empty.

Info View (Views)

27282 Movie Recorder: The values of Light Source Intensity, Channel name, and Dye name differ from those of snapped images. 34719 The entries of the fields FILTER, Laser Blanking and Beamsplitter are often empty for .lsm-images. 43225 The zoom factor used when acquiring images with AxioZoom or SteREO Discovery microscopes is not shown in the Info View. The pixel scale is correctly displayed however.

Microscopes and Stages (Devices)

27357 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 27821 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 and redefining tiles, positions or focus in the experiment.

Ortho View (Views)

37106 Orthoview does not work properly for large z-stack images acquired from multiples scenes. The slider position values in the Ortho Display view options tab represent the bounding box around all scenes while only one scene is being displayed. Workaround: splitting scenes into individual files (Processing/Utilities/Split scenes)

Physiology (Analysis)
43873 Activating the time line view panel during a running physiology experiment will result in the zoom setting of the Zoom tool control not been applied to the chart panels. Workaround: deactivate and secquently re-activate the time line view. Alternatively, press the Fixed button of the X-axis scaling controls. 43874 In the current release focal changes are not correctly updated in the physiology time line view panel. There is no workaround. 43886 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 ZEN 2012 SP1 (blue edition) Readme, March 2013 Page 8

allow the appropraite measurements to be made. Currently no warning message or infomation text is displayed to this effect.

Product related (General)

33383 FRAP events generated in ZEN blue edition are not interpreted correctly when opened in ZEN black edition. Workaround: redrawing the ROI's in ZEN black. 42561 Moving CZI images from ZEN Blue edition to ZEN Black edition or vice versa causes some meta data to be overwritten. When saving those files in the respective applications those metadata get lost potentially leading to lost information. Workaround: dragging images to the other application but not saving the images avoids the problem.

Simple interface (OAD)

43336 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.

Splitter document (Views)

41634 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.

Third Party Interaction (OAD)

39699 Due to some internal limitations, sending a singel channel image from ZEN to ImageJ or Fiji can using the Send To function results in an RGB image in ImageJ. Workaround: Opening the image directly within Fiji/ImageJ.

Tiles and Positions (Acquisition)

20751 It is not possible to modify a drawn grid because it is below the blue frame. Workaround: delete the grid and redraw again to the desired size. 24723 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 35135 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 rechecking tile regions /positions in different containers! 42619
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.

43590

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Channel settings metadata is mixed up or missing for saved preview scan images generated in the Tile tool Advanced set-up 43687 Panaroma with a motorised stage will does not work with Fast Acquisition in either the triggered or comprimised modes. Panorama should only be used with the Interactive acquisition mode. 43956 In the Tiles Advanced Setup - replication of tile regions with support point to all or multiple containers of a carrier is subject to a display update fault. As a workaround please leave then reopen the advance set-up to circumvent this issue.

User Management (General)

41197 It is possible to delete the user Admin from the list of administrators. This makes administration of the user management impossible. Solution: Deleting the user management data (C:\Users\<username>\AppData\Roaming\Carl Zeiss\ZEN\UserInformationLog.xml), this will reset the user management. ZIS Lite (General) 27062 The movie recording is not stopped when unplugging active camera. 32796 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.

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