zeiss zen 3.3 (blue edition)...1 zen 3.3 (blue edition) zeiss area / modulefeatures / improvements...

Release Notes

ZEISS ZEN 3.3 (blue edition)

ZEISS ZEN 3.3 (blue edition)

Original Manual

Carl Zeiss Microscopy GmbHCarl-Zeiss-Promenade 1007745 [email protected]/microscopy

Carl Zeiss Microscopy GmbHZEISS Group Kistlerhofstr. 75 81379 München

Document Name: ZEISS ZEN 3.3 (blue edition) Release NotesRevision: 1Language: en-USEffective from: 10/2020

© 2020 This document or any part of it must not be translated, reproduced, or transmitted in any form or by any means, elec-tronic or mechanical, including photocopying, recording, or by any information or retrieval system. Violations will be prose-cuted. The use of general descriptive names, registered names, trademarks, etc. in this document does not imply, even in theabsence of a specific statement, that such names are exempt from the relevant protective laws and regulations and thereforefree for general use. Software programs will fully remain the property of ZEISS. No program, documentation, or subsequent up-grade thereof may be disclosed to any third party, unless prior written consent of ZEISS has been procured to do so, nor may becopied or otherwise duplicated, even for the customer's internal needs, apart from a single back-up copy for safety purposes.

ZEISS reserves the right to make modifications to this document without notice.

1 ZEN 3.3 (blue edition) ZEISS

1 ZEN 3.3 (blue edition)

New ModulesThe following new software modules are available:

Module Description

Module 3Dxl plus This new module allows simultaneous viewing of 3D image data andits corresponding orthogonal 2D view planes. Rendering of up tothree 2D and one 3D view pane is possible in a single viewer. Featuresinclude:

§ Display of multidimensional image stacks as 3D volume models us-ing efficient ray tracing technology in the 3D panel.

§ 3Dxl plus is based upon the technology of arivis AG(www.arivis.com) and is suitable for rendering of extremely largeimages.

§ 3 rendering methods: Transparency, Volume, and Maximum. Theappearance of the rendering can be adjusted as required by chang-ing transparency, background and lighting parameters.

§ Ortho Display allows the adjustment of the cut line position andline width for each 2D pane independently.

§ The opacity of all displayed cut lines can be globally adjusted to op-timize the display of image details.

§ View layout can be changed by selecting between 6 present panelayout schemes. Alternatively, the pane size can be changed freelyand or the view assigned to a given pane modified as required toan individual preference.

New Features & Improvements

Area / Module Features / Improvements

Focus strategies A focus strategy wizard is now available if a tiles and positions experi-ment is activated.

LSM980 UI for control of new NLO lasersA software supported fine adjustment of the periscope for homoge-neous illumination and beam overlay (system maintenance and cali-bration) as well as new UI controls and parameter setting in Laser andchannels tool. More detailed information can be found on the CurioZwebsite.

Measurement Measurement features are now grouped (as in ZEN core) in the fol-lowing setup dialogs:

§ Feature Selection

§ Interactive Measurement Sequence Definition

Module Tiles & Po-sitions

The module tiles and positions includes the specialized focus strategyUse z-values/ Focus surface defined in Tiles Setup. This flexible,but in combination with Definite Focus and Software Autofocus,somewhat complex focus strategy now includes a focus strategy wiz-ard to help guide users to the correct settings by application and sam-ple characteristic-based questioning.

Release Notes ZEISS ZEN 3.3 (blue edition) | en-US | Rev.1 3



§ Works with z-stack and time series dimensions

§ Extended dedicated help information

Other new features include:

§ Drag and drop czi image files into the advanced tile setup fromwindows explorer or the image and documents tool

§ Create polygon tile regions in stake mode

§ Update z-values via context menu in advanced tile setup

§ Better high contrast positions flags

Module Direct Pro-cessing

The module Direct Processing has been improved and offers the fol-lowing new features:

§ Processing modules Deconvolution, Airyscan Processing and Apo-tome RAW Convert as well as processing functions Denoising andUnsharp Mask are available and can be setup in a pipeline so oneor more processing tasks can be selected as required, e.g. Apo-tome Raw Convert and Deconvolution.

§ The connection of acquisition and processing PC is now much eas-ier and much faster and works using a discovery proxy – this is thesame process by which a printer can be made available in networkand connected to with little effort.

§ The implementation also supports automatic selection of the pro-cessing PC should more than one be available. Direct processingwill select the best processing PC available, but also take any jobqueues into account when doing so. A manual selection can alsobe made by choosing from a list - each processing PC displays itsdetails and current workload.

§ Communication mode: removed file-based communication as net-work-based communication enhances flexibility and usability

Module Intellesis The module Intellesis has been improved and offers higher perfor-mance for the feature extraction process:

§ New parallelization concept for feature extraction when usingmodern multi-core machines. This results in speedup between 1.2xand 2.6x depending on algorithm in question.

§ Updated Python package index to create CZMODELs from exter-nally trained deep neural networks to be used inside ZEN blue.

§ Updated content of Machine Learning page on Github

§ Import from trained Deep Neural networks for Segmentationtrained on APEER by downloading the CZMODEL file

Module ImageAnalysis

The module Image Analysis has been improved and offers the follow-ing new features:

§ New measurement features include the metadata parameters Im-age Scene Name and Image Container Category. These fea-tures allow users to extract their results easily based on predefinedcategories assigned to a tile region like “Control” or “series A” orthe name assigned to it. This allows the data to be clearly struc-tured to ease evaluation of the results. Both these parameters areuser defined in the Tile Regions expander of the tiles tool prior toimage acquisition.




Module Macro En-vironment

Please note the following license check changes: From ZEN blue 3.3executing image processing functions that are available with Ad-vanced Processing or EM processing license will perform a licensecheck when executed from OAD.

Executing the functions list below from within OAD will now require avalid Advanced Processing license!

§ Arithmetic: Addition, AddConstant, Subtraction, Multiplication,MultiplyConstant, Negation (GUI: 'Invert'), Division, Square, Square-Root, Logarithm, Exponential, Inversion (GUI: 'Reciprocal'), Aver-age, Combine, Minimum, Maximum

§ Binary: FillHoles, Scrap, MarkRegions, ApplyMask, And, Or, Xor, In-vert, UltimateErode, Distance, Thinning, Exoskeleton, Separation,LabelImage

§ Filtering.Edges: Highpass, Roberts, GradientMax, GradientSum, So-bel, Laplace, LocalVariance - Morphology: Erode, Dilate, Open,Close, TopHatWhite, TopHatBlack, Gradient, Watersheds, GrayRe-construction

§ Segmentation: Threshold, ThresholdAutomatic, ThresholdDynamic,Valleys, Canny, Marr, RegionGrowing (not accessible via GUI)

§ Filtering.Smooth: Rank

§ Utilities: CombineHls, SplitHls, NoiseVariate

§ EM Processing: Coarse z-Stack alignment, Cut Out Regions, En-hance Local Contrast, Remove Stripes,Slices Replacement,SortSmartFIB Tiffs,Z-Stack Equalization

The following new features are now available with ZEN 3.3:

§ Autosave path is now available from OAD (e.g. for combinationwith Barcode reader)-Activate: exp.AutoSave.IsActivated = True-Name: exp.AutoSave.Name = "myexperiment„-Folder: exp.AutoSave.StorageFolder = "C:\\temp"

§ Close ZEN from TCP/IP gracefully. Note: be sure to save all opendocuments before executing this command.Zen.Application.Shutdown()

§ ZenTable can now be converted into a DataTable which offersmany methods to modify a table via IronPythontable1 = ZenTable()dtab = table1.ToDataTable()

§ Create and use subfolders in Macro Editor allowing users to groupmacros according to categories.

§ Import and open macros in Macro Editor via Drag& DropUpgradeof Iron Python to v. 2.7.10

Module ZEN DataStorage and Client

Enhanced gallery and image sorting and grouping functions are nowsupported. ZEN Connect projects can also now be listed, and perfor-mance enhancements allow large data sets (Axio scan) to be handledquickly for smooth interaction.

Module EM Pro-cessing Toolbox

Introduced with ZEN 3.2 in May 2020 this module for EM image pro-cessing applications now includes some additional functions. Bundlesmany known and new IP functions with focus on handeling SmartFIB(Cryo) images. New features in ZEN blue 3.3 include:




§ Import SmartFIB TIFFs: imports SmartFIB tiff image stacks and con-verts them to a czi-image.metadata is automatically read from theSmartFIB tiffs.

§ Macro Linear Drift Correction.czmac to compensate a linear driftin the image stack is available on the product DVD at: Other\OADexamples


Carl Zeiss Microscopy GmbHCarl-Zeiss-Promenade 1007745 JenaGermany

phone: +49 3641 64 3161fax: +49 3641 64 [email protected]/microscopy

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