ZEN Open Application Development (OAD) Tools for Smart...
Transcript of ZEN Open Application Development (OAD) Tools for Smart...
ZEN Open Application Development (OAD) Tools for Smart Microscopy
EuBIAS 2015, Paris, 2015-01-05
Dr. Sebastian Rhode
2 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
Agenda
1 2 3
4 5
ZEN Macro Interface
COM & TCP/IP Interface
ZEN Extensions
Experiment Feedback
OAD - Introduction and General Concept
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ZEN is only one part of the workflow
ZEN
Python OAD
Automation Analysis Fiji
KNIME
Scripting MATLAB
Simplify Extensions
Excel
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OAD – General Concept and Key Features
• Open Application Development (OAD) uses powerful Python Scripts inside ZEN Blue to simplify, customize and automate your workflows.
• The CZI-API, ZeissImageLib.dll (.NET) and BioFormats (CZIReader) allow
access to CZI files from external applications. • Analyze and Exchange your data with other external applications like Fiji,
Python, CellProfiler, MATLAB, Excel and …
• Create “smart” experiments with Exp. Feedback and Exp. Designer and modify the acquisition On-the-fly based on Online Image Analysis and External Inputs.
• Use Extensions to create your own applications and interfaces inside ZEN.
= Get more reliable results with less effort
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OAD – Concept and Interfaces
Sim
ple
Inte
rfac
e
Python Macro
Extensions
ZEN Application
Acquisition
Processing
Analysis
Measurement
CZI-Image
COM
TCP/IP Inte
rface
s
Zen Browser
Web-Viewing
ZEN Acq. Server
Exp. Feedback Python Scripts
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Agenda
1 2 3
4 5
ZEN Macro Interface
COM & TCP/IP Interface
ZEN Extensions
Experiment Feedback
OAD - Introduction and General Concept
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ZEN Macro Interface
Simple Interface
Python IDE
• Recorder • Editor • Debugger
Macro Interface
ZEN Application
IronPython
.Net based (managed code)
Your Choice .Net Framework IronPython
Standard Library
Other Python Libraries*
Other .Net DLL
* With support of IronPython
import
Basic Libraries
Third Party Customized Solution
Start External Apps or Scripts Exchange Data
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Macro Workflow Example – Part 1
Acquisition
Processing
Analysis
Measurement
Settings File (XML)
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Macro Workflow Example – Part 2
IronPython Standard Library .Net Framework
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Use External Image Analysis from ZEN …
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… reimport the results into ZEN and proceed
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Agenda
1 2 3
4 5
ZEN Macro Interface
COM & TCP/IP Interface
ZEN Extensions
Experiment Feedback
OAD - Introduction and General Concept
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COM & TCP/IP Interface
Simple Interface
Application
COM Interface
ZEN Application
COM Interface
e.g. Python, MATLAB, Excel
Simple Interface
ZEN Application
TCP/IP Listener
Application
TCP/IP Interface
e.g. PuTTY
ZEN as a „Server“ Client
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ZEN Remote via COM Interface - Python
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ZEN Remote via COM Interface – Python 1
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ZEN Remote via COM Interface – Python 2
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Read CZI directly via Python BioFormats and process the data
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ZEN Remote via COM Interface - MATLAB
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Agenda
1 2 3
4 5
ZEN Macro Interface
COM & TCP/IP Interface
ZEN Extensions
Experiment Feedback
OAD - Introduction and General Concept
20 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
ZEN Extensions Interface
ZEN
ZEN - Extension Manager
ZEN - LeftToolArea
SharpDevelop
‚Third Party‘ Area
Place your extension here…
.dll Interface
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ZEN Extensions - Examples
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Agenda
1 2 3
4 5
ZEN Macro Interface
COM & TCP/IP Interface
ZEN Extensions
Experiment Feedback
OAD - Introduction and General Concept
23 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
Exp. Feedback – Adaptive Acquistion Engine
Import modules & define actions at the beginning of the experiment.
Set up rules & actions to be executed during the experiment in a loop. • React upon results from online image analysis
and external inputs • Modify the running experiment on-the-fly
Define actions to be taken when the experiment stops.
Observe
Actions
Tools
Select Online Image Analysis
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Exp. Feedback – Adaptive Acquistion Engine
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Exp. Feedback Example – Analyze Online
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www.zeiss.com/czi
www.zeiss.com/zen-oad