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University Division/Office 
15.04.15 
Page 1 
Automation of repetitive image 
processing tasks by macro 
scripting in ImageJ / Fiji 
Lunch Seminar Series in Microscopy and Image Processing 
Moritz Kirschmann 
Moritz.kirschmann@zmb.uzh.ch 
Center for Microscopy and Image Analysis 
Extract photos from pdf - Select, copy, paste PDF images in C#.net, ASP.NET, MVC, Ajax, WinForms, WPF
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Support PDF Image Extraction from a Page, a Region on a Page, and PDF Document
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Table of Contents 
1)  Introduction to Fiji 
2)  Functionality of Fiji  
3)  Batch conversion 
4)  Recording and writing macros 
5)  Where to find more info 
VB Imaging - VB ISSN Barcode Generating
help VB.NET developers draw and add standard ISSN barcode on photos, images and BMP image formats, our users can even create ISSN barcode on PDF, TIFF, Excel
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C# Image: How to Add Antique & Vintage Effect to Image, Photo
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1. Fiji 
-  A distribution of ImageJ including many useful plug-ins for life sciences 
-  Open source 
-  Written in Java 
-  Under GNU General Public License 
-  Runs on Windows, MacOS, Linux 
-  Under daily development by a large community 
VB.NET TWAIN: Scanning Multiple Pages into PDF & TIFF File Using
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VB.NET Image: Program for Creating Thumbnail from Documents and
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2. Functionality of Fiji and its plug-ins 
-  Reads many data formats (TIF, JPG, PNG, …), including proprietary  
formats (CZI, LIF, DM3, DM4, STK, ICS, IMS, …) 
-  Image contrast and look-up-table modifications 
-  Modification of metadata such as pixel sizes 
-  Maximum intensity projections of image stacks  
-  Segmentation 
-  Counting objects 
-  Measuring intensities, length, areas, shape parameters and more…  
-  Reconstruct objects from serial section 
-  Visualize in 3D 
-  […] 
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VB.NET Image: Barcode Reader SDK, Read Intelligent Mail from Image
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University of Zurich, Division/Office, Title of the presentation, Author 
Page 5 
Show menus of Fiji 
VB.NET Image: VB Code to Read Linear Identcode Within RasterEdge .
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2. Functionality of Fiji and its plug-ins 
-  Reads many data formats (TIF, JPG, PNG, …), including proprietary  
formats (CZI, LIF, DM3, DM4, STK, ICS, IMS, …) 
-  Image contrast and look-up-table modifications 
-  Modification of metadata such as pixel sizes 
-  Maximum intensity projections of image stacks  
-  Segmentation 
-  Counting objects 
-  Measuring intensities, densities, shape parameters of segments 
-  Reconstruct objects from serial section 
-  Visualize in 3D 
-  […] 
-  Batch functions 
C# Imaging - Scan RM4SCC Barcode in C#.NET
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VB.NET Image: Image Resizer Control SDK to Resize Picture & Photo
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University of Zurich, Division/Office, Title of the presentation, Author 
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3. Demo – Batch conversion 
Scenario: preparing many images for website 
publishing by scaling down and compressing 
lossy as JPG 
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Functionality of Fiji and its plug-ins 
-  Reads many data formats (TIF, JPG, PNG, …), including proprietary  
formats (CZI, LIF, DM3, DM4, STK, ICS, IMS, …) 
-  Image contrast and look-up-table modifications 
-  Modification of metadata such as pixel sizes 
-  Maximum intensity projections of image stacks  
-  Segmentation 
-  Counting objects 
-  Measuring intensities, densities, shape parameters of segments 
-  Reconstruct objects from serial section 
-  Visualize in 3D 
-  […] 
-  Batch functions 
-  Scriptable 
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University of Zurich, Division/Office, Title of the presentation, Author 
Page 9 
4.1 Demo – Recording a macro 
Scenario: Correct the scaling of images 
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University of Zurich, Division/Office, Title of the presentation, Author 
Page 10 
4.2 Demo – Recording a macro 
Scenario: You acquired image stacks with multiple 
channels and you need to display all channels at 
the same time and make a projecting the z-axis. 
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