Curtis Rueden, UW-Madison LOCI
https://imagej.github.io/presentations/2017-06-01-imagej2-loci
LOCI develops advanced optical and computational techniques for imaging and experimentally manipulating living specimens.
// Create a new ImageJ gateway with all available services.
ij = new ImageJ()
// Load a dataset from somewhere.
dataset = ij.io().open(imageSource)
// Filter the image.
fft = ij.op().fft(dataset)
lowpass(fft, 10)
result = ij.op().ifft(fft)
// Display the result.
ij.ui().show(result)
"Write once, run anywhere" image processing
Schindelin, J., et al. "The ImageJ ecosystem: an open platform for biomedical image analysis." Molecular reproduction and development 82.7-8 (2015): 518-529.
Why use ImageJ? Why improve ImageJ?
Why not use Imaris and MATLAB for everything?
Why join this community?
Why do science in the first place?
Is this a good segmentation?
(source)
Using 'Otsu' I find --- not a little difference --- but a big one. A little difference caused by the binning, a big one between implementations. Which is the 'real' Otsu threshold?
—Robert Atwood (source)
The Otsu algorithm had indeed an issue only with certain 16bit histograms where the computation of the variance could cause an overflow that carried on without triggering an error. I checked Emre Celebi's library (Fourier 0.8) and his C++ version does not have the problem so I replaced the previous version with Emre's. 8 bit images were not affected. I just checked and it finds the ball in your sample image now.
The Huang method is a different issue. The original code by Emre was rewritten in 2011 by Johannes Schindelin to use more efficiently the 16bit data and has a massive execution speed advantage. However I just noted that in some cases it does return exactly the same values as the original even in some 8bit images. I therefore added back the original code and kept Johannes' method as "Huang2" for the time being until I have time to look at it in more depth.
I also found that the Mean method (again in 16bits only) had a potential for overflow that could go without triggering errors, so I fixed that too.
—Gabriel Landini (source)
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Publish a compendium, not just a result
"An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship."
—David Donoho, "Wavelab and Reproducible Research," 1995
Deep reproducibility demands the source code
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And it is good for your career:
"Papers describing software published as open source are amongst the most widely cited publications (e.g., BLAST, and Clustal-W), suggesting many scientific studies may not have been possible without some kind of open software to collect observations, analyze data, or present results."
—Andreas Prlić & James Procter
"Ten Simple Rules for the Open Development of Scientific Software"
And it is good for your career:
"Science is hard enough already."
—Andreas Prlić & James Procter
"Ten Simple Rules for the Open Development of Scientific Software"
And it is good for your career:
Seriously.
^ Look familiar? ;-)
ImageJ2
SciJava
(base)
ImgLib2
(data model)
SCIFIO
(image I/O)
Ops
(image processing)
ImageJ Legacy
(compatibility)
A pledge to cooperate and reuse code
A collection of software components curated together
A promise of compatibility
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Image types | uint8, uint16, float32, rgb | bit, uint2, uint4, uint8, uint12, uint16, uint32, uint64, uint128, int8, int16, int32, int64, float32, float64, cfloat32, cfloat64, bigint, bigdec, argb, <your-image-type-here> |
Plugin types | PlugIn, PlugInFilter, PlugInTool | Command, Op, Tool, IOPlugin, Service, Converter, Codec, Format, DataHandle, TextFormat, ScriptLanguage, Display, UserInterface, Platform, App, Gateway, ModulePreprocessor, ModulePostprocessor, CodeRunner, ..., <your-plugin-type-here> |
Dimensions | 5D—XYZCT | N-dimensional—X, Y, Z, time, channel, emission spectra, lifetime, cell polarity, <your-dimension-here> |
Image formats | HandleExtraFileTypes | SCIFIO—including Bio-Formats plugin; <your-format-here> |
Parameters | GenericDialog | SciJava module @ parameter syntax—callable from ImageJ, KNIME, OMERO, CellProfiler, ..., <your-tool-here> |
Script languages | IJ1 macro, JavaScript, BeanShell, Java | BeanShell, Clojure (Lisp), Groovy, Java, JavaScript, JRuby, Jython (Python), Renjin (R), Scala, <your-language-here> |
User interface | AWT | Legacy, Swing, AWT, Apache Pivot, Eclipse SWT, JavaFX, KNIME, CellProfiler, OMERO, <your-ui-here> |
Distribution | Download, install and update manually | Hundreds of update sites; receive updates automatically (when you want!) |
"Of course there is plans..."
—Florian Jug
Help others to avoid repeating your pain.
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Academic paper
Rueden, C. T., et al. "ImageJ2: ImageJ for the next generation of scientific image data." arXiv preprint (2017).
45-minute presentation
Rueden, C. T. "ImageJ2 and Fiji: The ImageJ2 platform, and the Fiji distribution of ImageJ." ImageJ Conference 2015. video, slides
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And all supporters of open science and open software!