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


ZEN is only one part of the workflow

ZEN

Python OAD

Automation Analysis Fiji

KNIME

Scripting MATLAB

Simplify Extensions

Excel


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

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


Agenda

1 2 3

4 5

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

1 2 3

4 5

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

https://ixquick-proxy.com/do/show_picture.pl?l=deutsch&cat=pics&c=pf&q=microsoft+excel&h=577&w=577&th=160&tw=160&fn=microsoft_excel_2010.png&fs=33.2%20k&el=boss_pics_2&tu=http://ts2.mm.bing.net/th?id%3DHN.608009739830362969%26pid%3D15.1%26H%3D160%26W%3D160&rl=NONE&u=http://www.brandsoftheworld.com/logo/microsoft-excel-2010?original%3D1&udata=07a14d1f4dfed59077145d14429c282c&rid=LGLOLLTSPMQR&oiu=http://www.brandsoftheworld.com/sites/default/files/styles/logo-original-577x577/public/042011/microsoft_excel_2010.png

https://ixquick-proxy.com/do/show_picture.pl?l=deutsch&cat=pics&c=pf&q=putty+tcp+client&h=514&w=500&th=164&tw=160&fn=500px-TEL0047_Fig4_Putty_config.PNG&fs=157.7%20k&el=boss_pics_1&tu=http://ts2.mm.bing.net/th?id%3DHN.607993955824960925%26pid%3D15.1%26H%3D164%26W%3D160&rl=NONE&u=http://www.dfrobot.com/wiki/index.php/WiFi_Shield_V2.2_For_Arduino_(SKU:TEL0047)&udata=a131d382db7534e282a1accb1fc541f0&rid=NDLOLLTSPNPP&oiu=http://www.dfrobot.com/wiki/images/thumb/1/11/TEL0047_Fig4_Putty_config.PNG/500px-TEL0047_Fig4_Putty_config.PNG


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

1 2 3

4 5

ZEN Macro Interface


ZEN Extensions

Experiment Feedback



ZEN Extensions Interface

ZEN

ZEN - Extension Manager

ZEN - LeftToolArea

SharpDevelop

‚Third Party‘ Area

Place your extension here…

.dll Interface


ZEN Extensions - Examples


Agenda

1 2 3

4 5

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

Tools

Select Online Image Analysis


Exp. Feedback – Adaptive Acquistion Engine


Exp. Feedback Example – Analyze Online


www.zeiss.com/czi

www.zeiss.com/zen-oad

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