ZEN Open Application Development (OAD) Tools for Smart Microscopy EuBIAS 2015, Paris, 2015-01-05 Dr. Sebastian Rhode
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
3 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
ZEN is only one part of the workflow
ZEN
Python OAD
Automation Analysis Fiji
KNIME
Scripting MATLAB
Simplify Extensions
Excel
4 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
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
5 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
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
6 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
7 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
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
8 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
Macro Workflow Example – Part 1
Acquisition
Processing
Analysis
Measurement
Settings File (XML)
9 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
Macro Workflow Example – Part 2
IronPython Standard Library .Net Framework
10 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
Use External Image Analysis from ZEN …
11 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
… reimport the results into ZEN and proceed
12 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
13 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
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
14 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
ZEN Remote via COM Interface - Python
15 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
ZEN Remote via COM Interface – Python 1
16 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
ZEN Remote via COM Interface – Python 2
17 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
Read CZI directly via Python BioFormats and process the data
18 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
ZEN Remote via COM Interface - MATLAB
19 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
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
21 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
ZEN Extensions - Examples
22 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
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
24 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
Exp. Feedback – Adaptive Acquistion Engine
25 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
Exp. Feedback Example – Analyze Online
26 2015-01-03 Carl Zeiss Microscopy GmbH, Dr. Sebastian Rhode
www.zeiss.com/czi
www.zeiss.com/zen-oad