Suite for ImageJ Paul Cueva, David A. Muller pdc23@cornell.edu - - PowerPoint PPT Presentation

Open Source Hyperspectral Data Analysis Suite for ImageJ Paul Cueva, David A. Muller pdc23@cornell.edu

ImageJ

• Started as NIH Image by Wayne Rasband before 1993

ImageJ created in 1997 Fiji packaged started in 2007 ImageJ2 released in 2009

11/16/2018 Nion Swift Workshop IV - Paul Cueva – CSI 2

ImageJ

• Started as NIH Image by Wayne Rasband before 1993

ImageJ created in 1997 (12440 citations) Fiji packaged started in 2007 (7205 citations) ImageJ2 released in 2009 (107 citations)

11/16/2018 Nion Swift Workshop IV - Paul Cueva – CSI

Rueden, C. T. et al. (2017), BMC Bioinformatics 18:529 Schneider, C. A. et al. (2012), Nature methods 9(7): 671-675 Schindelin, J. et al. (2012), Nature methods 9(7): 676-682

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• Fiji currently packaged with 247 plugins

~10% are specific for the life sciences The rest are general image processing features None for physical sciences

• Part of the SciJava community

The Standard in Biological Sciences

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• Community of scientific

computing software for Java

• Most important

integration with Fiji is Bio-Formats, & OMERO

SciJava

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• Hosts data & analysis on the cloud
• Allows for collaboration
• Upon publication allows for scientific

repeatability of analysis

Open Microscopy

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• Benchmarks (supposedly) show no

appreciable slow down

– "Java often outperforms C++ in operations such as memory allocation and file I/O while C++ often

• utperforms Java in arithmetic and trigonometric
• perations."
• Geared for UI (Swing)
• User friendliness, portability, & history

Why Java?

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http://www.drdobbs.com/cpp/microbenchmarking-c-c-and-java/184401976

• Matrix libraries/linear algebra won’t stay alive!
• Jama (no update in 6 years)
• UJMP (no update in 3 years)
• Apache Commons Math

(missing some functionality)

• ojAlgo live & fast

(but annoying)

Why?? Java

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Cornell Spectrum Imager

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Cornell Spectrum Imager

11/16/2018 Nion Swift Workshop IV - Paul Cueva – CSI

• CSI first released as a standalone distribution of

ImageJ1 in 2011 (60 citations)

• 4D analysis added in 2016 with the

Multidimensional Imaging Analysis and Management Interface

• Version 2.0 released in 2017 as a Fiji plugin

Cueva, P. et al. (2012), Microscopy & Microanalysis 18(4): 667-675

CSI:MIAMI

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Getting CSI:MIAMI

11/16/2018 Nion Swift Workshop IV - Paul Cueva – CSI

• Source code:

https://github.com/pdcueva/cornell-spectrum-imager

• Installation

– Download Fiji http://http://fiji.sc/ – Select Help>Update… – Click Manage update sites – Add update site – Enter url: http://sites.imagej.net/CSI/

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Future of CSI

11/16/2018 Nion Swift Workshop IV - Paul Cueva – CSI

• Significant room for speed ups

(ojAlgo implementation, smarter processing, iterative SVD)

• Acquisition via integration with μManager
• Jython scripting

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Conclusions & Thoughts for Nion Swift

11/16/2018 Nion Swift Workshop IV - Paul Cueva – CSI

• CSI:MIAMI is an open source plugin suite for Fiji

that democratizes EELS & 4D-STEM analysis

– Light-weight companion to Nion Swift – Microsoft Office vs LaTeX

• Nion Swift

– Integration with other open science platforms – 4D analysis approaches

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