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

ZEN Macro Interface

COM & TCP/IP Interface

ZEN Extensions

Experiment Feedback

OAD - Introduction and General Concept

ZEN is only one part of the workflow

Python OAD

Automation Analysis Fiji

Scripting MATLAB

Simplify Extensions

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

OAD – Concept and Interfaces

Python Macro

Extensions

ZEN Application

Acquisition

Processing

Analysis

Measurement

CZI-Image

TCP/IP Inte

Zen Browser

Web-Viewing

ZEN Acq. Server

Exp. Feedback Python Scripts

Agenda

ZEN Macro Interface

ZEN Extensions

Experiment Feedback

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

Macro Workflow Example – Part 1

Acquisition

Processing

Analysis

Measurement

Settings File (XML)

Macro Workflow Example – Part 2

IronPython Standard Library .Net Framework

Use External Image Analysis from ZEN …

… reimport the results into ZEN and proceed

Agenda

ZEN Macro Interface

ZEN Extensions

Experiment Feedback

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

ZEN Remote via COM Interface - Python

ZEN Remote via COM Interface – Python 1

ZEN Remote via COM Interface – Python 2

Read CZI directly via Python BioFormats and process the data

ZEN Remote via COM Interface - MATLAB

Agenda

ZEN Macro Interface

ZEN Extensions

Experiment Feedback

ZEN Extensions Interface

ZEN - Extension Manager

ZEN - LeftToolArea

SharpDevelop

‚Third Party‘ Area

Place your extension here…

.dll Interface

ZEN Extensions - Examples

Agenda

ZEN Macro Interface

ZEN Extensions

Experiment Feedback

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

Select Online Image Analysis

Exp. Feedback – Adaptive Acquistion Engine

Exp. Feedback Example – Analyze Online

www.zeiss.com/czi

www.zeiss.com/zen-oad

ZEN Open Application Development (OAD) Tools for Smart...

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Transcript of ZEN Open Application Development (OAD) Tools for Smart...

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