ImageJ2 and Fiji

The ImageJ2 platform

The Fiji distribution of ImageJ

Curtis Rueden, UW-Madison LOCI

Tweets to #imagej2015

A colleague told me once:

It's not the code that matters—it's the community.

But you can't build a house with your bare hands.

Well, maybe you can...

...but there are limits.

You can't build a house alone, either.

Tools, and people to create
and use them, are both necessary.

But wait...

Creating software is not like building a house!
It's more like designing a house.
Once designed, you can mass produce it.
But the design keeps changing...
Is this analogy even helpful anymore?
No more analogies!

A brief history of ImageJ

http://imagej.net/History

1997
2007
2009
2011

ImageJ2 milestones

http://imagej.net/news

2011	Update sites
2012	First ImageJ2 beta version
2013	Personal update sites
2014	Fiji Is Just ImageJ2
	ImgLib2 comes out of beta
	Fiji builds become reproducible
2015	Several major goals

ImageJ2's Mission

Create the next ImageJ, based on community needs
Collaborate with others whenever beneficial
Make ImageJ useful to a broad community
Maintain backwards compatibility with ImageJ 1.x
Provide a central online resource for ImageJ
Lead ImageJ development with a clear vision

Create the next ImageJ, based on community needs
Collaborate with others whenever beneficial
Make ImageJ useful to a broad community
Maintain backwards compatibility with ImageJ 1.x
Provide a central online resource for ImageJ
Lead ImageJ development with a clear vision

DESIGN
COLLABORATE
BROADEN
MAINTAIN
UNIFY
LEAD

BLUE = Architectural

RED = Technical

Create the next version of ImageJ, based on the needs of the community

What's great about ImageJ?

Extensibility
Available functions

What else is needed?

Generality [1, 2]
Modularity [3]
Interoperability+integration [4]
More extensibility! [5]

Create the next version of ImageJ, based on the needs of the community

What is ImageJ2?

An end-user application


/** Loads and displays a dataset using the ImageJ API. */
public void loadAndDisplayDataset(final File file) {
	// create the ImageJ application context with all available services
	final ImageJ ij = new ImageJ();

	// load the dataset
	final Dataset dataset = ij.scifio().datasetIO().open(file.getAbsolutePath());

	// display the dataset
	ij.ui().show(dataset);
}

A reusable library

An extensible collection
of services & plugins

"Write once, run anywhere"
image processing routines

A new, supremely extensible plugin framework
Dimensions beyond X, Y, Z, time and channel
Planes larger than 2 gigapixels
Pixel types beyond uint8, uint16 and float32
Access data beyond only files on disk
Beyond one user, one desktop, one machine

An effort to overcome
the constraints of ImageJ

Create the next version of ImageJ, based on the needs of the community

Components of ImageJ2

http://imagej.net/ImageJ2

ImageJ

Image-specific components

SCIFIO

http://imagej.net/SciJava_Common

More general than images

Application container
Plugin framework
Module framework
Display and UI frameworks
Scripting framework and plugins

http://imagej.net/Architecture

Collaborate with others whenever beneficial

The SciJava consortium

Kevin
Eliceiri

Jason
Swedlow

Pavel
Tomancak

Anne
Carpenter

Michael
Berthold

Christian
Dietz

Mark
Hiner

Lee
Kamentsky

Brian
Northan

Tobias
Pietzsch

Stephan
Preibisch

Curtis
Rueden

Stephan
Saalfeld

Johannes
Schindelin

And everyone supporting open science + open software!

Collaborate with others whenever beneficial

The SciJava pledge

Work together, reuse code and synergize

Collaborate with others whenever beneficial

Interoperability + integration

SciJava Modules: parameterized commands and scripts


@Parameter(label="Input image")
private ImagePlus original;

@Parameter(label="Sigma")
private double sigma = 1.0;

@Parameter(label="Use calibration")
private boolean useCalibration;

@Parameter(type=ItemIO.OUTPUT, label="Output image")
private ImagePlus result;

Make ImageJ useful to a broad community

Who is the target audience?

Scientific users
Casual users
Software developers
Image processing experts

Need rapid iteration + communication

Make ImageJ useful to a broad community

Separation of concerns

Migrate non-life-sciences code from Fiji to ImageJ2
Migrate image processing algorithms to ImageJ Ops
Broaden the image metadata model beyond microscopy
Migrate non-image-specific code from ImageJ to SciJava Common

Make ImageJ useful to a broad community

http://imagej.net/ImgLib2

http://imagej.net/Ops

N-dimensional data model

ImageJ Ops

"Write once, run anywhere" image processing

Powerful and general
Easy to use and extend
Good performance


# @OpService ops
ops.help("math.add")


(ArrayImg image) =
net.imagej.ops.math.add.AddConstantToArrayDoubleImageP(
	ArrayImg image,
	double value)
(ArrayImg image) =
net.imagej.ops.math.add.AddConstantToArrayByteImageP(
	ArrayImg image,
	byte value)
(ArrayImg image) =
net.imagej.ops.math.add.AddConstantToArrayDoubleImage(
	ArrayImg image,
	double value)
(ArrayImg image) =
net.imagej.ops.math.add.AddConstantToArrayByteImage(
	ArrayImg image,
	byte value)
(Img out?) =
net.imagej.ops.math.add.AddIterableIntervalToImg(
	Img out?,
	Img in,
	IterableInterval ii)
(int result) =
net.imagej.ops.math.PrimitiveMath$IntegerAdd(
	int a,
	int b)
(long result) =
net.imagej.ops.math.PrimitiveMath$LongAdd(
	long a,
	long b)
(float result) =
net.imagej.ops.math.PrimitiveMath$FloatAdd(
	float a,
	float b)
(double result) =
net.imagej.ops.math.PrimitiveMath$DoubleAdd(
	double a,
	double b)
(IterableRealInterval image) =
net.imagej.ops.math.add.AddConstantToImageInPlace(
	IterableRealInterval image,
	NumericType value)
(IterableInterval a) =
net.imagej.ops.math.add.AddRandomAccessibleIntervalToIterableInterval(
	IterableInterval a,
	RandomAccessibleInterval b)
(PlanarImg image) =
net.imagej.ops.math.add.AddConstantToPlanarDoubleImage(
	PlanarImg image,
	double value)
(RealType out) =
net.imagej.ops.math.RealMath$Add(
	RealType out,
	RealType in,
	double constant)
(RealType out?) =
net.imagej.ops.math.RealBinaryMath$Add(
	RealType out?,
	RealType in,
	RealType b)
(NumericType out?) =
net.imagej.ops.math.add.AddConstantToNumericType(
	NumericType out?,
	NumericType in,
	NumericType value)
(RandomAccessibleInterval out) =
net.imagej.ops.math.add.AddConstantToImageFunctional(
	RandomAccessibleInterval out,
	IterableInterval in,
	NumericType value)

Maintain backwards compatibility with ImageJ1

Maintain backwards compatibility with ImageJ1

http://imagej.net/Compatibility

ImageJ2 is ImageJ 1.x, plus the new stuff

ImageJ2 includes ImageJ version 1.x
ImageJ2 user interfaces (UIs) are plugins
ImageJ2's LegacyUI = ImageJ 1.x as a plugin
IJ1 and IJ2 data structures are translated on the fly
"Mix and match" ImageJ 1.x and ImageJ2 capabilities

Maintain backwards compatibility with ImageJ1

http://imagej.net/Versioning

Maintaining the stack

Everything on GitHub
Versioned with SemVer
Organized using a Bill of Materials
NEW: the SciJava melting pot

Provide central online resources for ImageJ

Plugins

http://imagej.nih.gov/ij/plugins/
http://imagejdocu.tudor.lu/doku.php?id=plugin:start
http://fiji.sc/Category:Plugins
http://imagej.nih.gov/ij/plugins/mbf/
http://sourceforge.net/projects/ij-plugins/
And dozens of other lists and collections

http://imagej.net/List_of_update_sites/
http://sites.imagej.net/

Provide central online resources for ImageJ

Online resources

imagej.net	primary portal
mirror.imagej.net	ImageJ 1.x website
wiki.imagej.net	ImageJ documentation
search.imagej.net	towards a unified search
sites.imagej.net	personal update sites

Provide central online resources for ImageJ

Developer resources

javadoc.imagej.net	developer documentation
status.imagej.net	tracking releases
maven.imagej.net	release binaries
jenkins.imagej.net	continuous integration

Lead ImageJ development with a clear vision

Managing expectations

Lead ImageJ development with a clear vision

The future of ImageJ

Lead ImageJ development with a clear vision

ImageJ2 and Fiji

The ImageJ2 platform The Fiji distribution of ImageJ

Well, maybe you can...

...but there are limits.

You can't build a house alone, either.

Tools, and people to createand use them, are both necessary.

But wait...

A brief history of ImageJ

ImageJ2 milestones

ImageJ2's Mission

GOLD = Social

BLUE = Architectural

RED = Technical

What's great about ImageJ?

What else is needed?

What is ImageJ2?

An end-user application

A reusable library

An extensible collectionof services & plugins

"Write once, run anywhere"image processing routines

An effort to overcomethe constraints of ImageJ

Components of ImageJ2

The SciJava consortium

The SciJava pledge

Interoperability + integration

Who is the target audience?

Need rapid iteration + communication

Separation of concerns

N-dimensional data model

ImageJ Ops

"Write once, run anywhere" image processing

ImageJ2 is ImageJ 1.x, plus the new stuff

Maintaining the stack

Plugins

Online resources

Developer resources

Managing expectations

The future of ImageJ

Join us!

The ImageJ2 platform

The Fiji distribution of ImageJ

Tools, and people to create
and use them, are both necessary.

An extensible collection
of services & plugins

"Write once, run anywhere"
image processing routines

An effort to overcome
the constraints of ImageJ