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

ImageJ • Started as NIH Image by Wayne Rasband before 1993 ImageJ created in 1997 (12440 citations) Schneider, C. A. et al. (2012), Nature methods 9(7) : 671-675 Fiji packaged started in 2007 (7205 citations) Schindelin, J. et al. (2012), Nature methods 9(7) : 676-682 ImageJ2 released in 2009 (107 citations) Rueden, C. T. et al. (2017), BMC Bioinformatics 18:529 Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 3

The Standard in Biological Sciences • 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 Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 4

SciJava • Community of scientific computing software for Java • Most important integration with Fiji is Bio-Formats, & OMERO Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 5

Open Microscopy • Hosts data & analysis on the cloud • Allows for collaboration • Upon publication allows for scientific repeatability of analysis Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 6

Why Java? • Benchmarks (supposedly) show no appreciable slow down – "Java often outperforms C++ in operations such as memory allocation and file I/O while C++ often outperforms Java in arithmetic and trigonometric operations." http://www.drdobbs.com/cpp/microbenchmarking-c-c-and-java/184401976 • Geared for UI (Swing) • User friendliness, portability, & history Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 7

Why?? Java • 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) Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 8

Cornell Spectrum Imager Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 9

Cornell Spectrum Imager • CSI first released as a standalone distribution of ImageJ1 in 2011 (60 citations) Cueva, P. et al. (2012), Microscopy & Microanalysis 18(4) : 667-675 • 4D analysis added in 2016 with the CSI:MIAMI Multidimensional Imaging Analysis and Management Interface • Version 2.0 released in 2017 as a Fiji plugin Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 10

Getting CSI:MIAMI • 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/ Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 11

Future of CSI • Significant room for speed ups (ojAlgo implementation, smarter processing, iterative SVD) • Acquisition via integration with μ Manager • Jython scripting Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 12

Conclusions & Thoughts for Nion Swift • 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 Nion Swift Workshop IV - Paul Cueva – CSI 11/16/2018 13