#BigDataViewer

2024-11-10

Hehe, the first game of life I code (in
using
obviously). Naive implementation, but still functionally defined and lazy computed - see how the data arrives as I scroll, and is cached.

2024-11-01

A tradition - showing off with This time by making the ABBA (go.epfl.ch/abba) logo with 4900 multiresolution images, each with a custom affine transform. Smooth when zoomed in, lagging a bit from afar but still very manageable.

2024-11-01

A classic in dynamical systems: the Lorenz attractor, computed and visualized using in

2024-11-01

Too lazy for a movie today, but look at this nice procedural image! It's a plane wave spherically transformed 2 times. Still with

2024-11-01

Spherical coordinates live transformation with .

Left: a view of a drosophila egg chamber, with a fitted ellipsoid on top of it,

right: a theta / phi view of the egg chamber. I also scroll along the r dimension, and rotate the poles.

2024-11-01

Another day, another
video. This time an orthoviewer + a BigVolumeViewer. Dataset = Allen Brain Atlas CCFv3.

All those demos will be accessible in Fiji with the PTBIOP update site soon.

2024-11-01

Yep, it lags a little. But still quite impressive considering that each "pixel" is a 150 MPixel multires image. Overall the total number of 'adressable' pixels in this 2D image are 225x225x150 Mpix = 7.6 Tera pixels.

2024-01-09

Why would one want to run machine learning inference from #java?

To do so on 3D, 4D, ND datasets, trivially accessible from image processing and visualization libraries such as #ImgLib2, the #BigDataViewer, #LabKit and more, all integral parts of #FijiSc.

* LabKit: imagej.net/plugins/labkit/

* BigDataViewer: imagej.net/plugins/bdv/

* ImgLib2: imagej.net/libs/imglib2/

* Fiji: fiji.sc

Mark Kittisopikulmarkkitti@fosstodon.org
2022-11-30

#FIJI development is mainly concentrated at #LOCI based at #UWMadison.

#imglib2 development is currently focused at @HHMI Janelia where I work.

Tobias Pietzsch, an independent developer, is now picking up of #imglib2 and #BigDataViewer development with support from #CZI and @HHMI .

Stephan Saalfeldherrsaalfeld@qoto.org
2022-11-29

If you happen to own the cheap but amazing Behringer X-TOUCH mini #MIDI controller, you can use it to navigate in #Fiji 's #N5 #BigDataViewer plugin. The video is an older capture from when I was playing around with the controller but it work's exactly the same. The API works for all #MCU devices but you would have to provide the layout github.com/saalfeldlab/n5-view (also, infinity VPots without physical min and max are useful for this). PRs welcome!

2022-11-02

Now onto #FijiSc: Fiji is a recursive acronym meaning "Fiji is just ImageJ" fji.sc (and the paper nature.com/articles/nmeth.2019 ) –and #ImageJ is a #java open source software for image processing imagej.nih.gov/ij/index.html written by Wayne Rasband from the #NIH Research Branch.

An analogy: think of ImageJ as the kernel and Fiji as the rest of the operating system.

#FijiSc brings to #ImageJ:
(1) a package manager to install and update plugins, and that crucially enables reproducible science by exporting the whole set of plugins and libraries as an executable;
(2) a Script Editor imagej.net/scripting/script-ed supporting many languages (#python, #groovy #ruby #scala #clojure and more), all with access to a huge collection of #JVM libraries;
(3) huge amount of libraries such as #ImgLib2, #JFreeChart for plotting, for GUIs, etc.

There are many, many plugins. A tiny sample:

Machine learning-based image segmentation:
- #LabKit imagej.net/plugins/labkit/
- #WEKA Trainable Segmentation imagej.net/plugins/tws/index

3D/4D/ND Visualization:
- 3D/4D Viewer #3DViewer imagej.net/plugins/3d-viewer/i with ray-tracing, orthoslices, volume rendering, and more
- #BigDataViewer #BDV imagej.net/plugins/bdv/index for interactively navigate N-dimensional image volumes larger than RAM

Image registration and serial section alignment:
- #BigStitcher for registering 3D/4D tiled datasets, with multiview deconvolution and more imagej.net/plugins/bigstitcher
- #TrakEM2 for montaging in 2D and alinging in 3D collections of serial sections, typically from #vEM (volume electron microscopy) syn.mrc-lmb.cam.ac.uk/acardona
- #mpicbg libraries for extracting #SIFT and #MOPS features, then finding feature correspondences and estimating rigid and elastic transformation models nature.com/articles/nmeth.2072

Summarizing #FijiSc is impossible. See the online forum where questions find answers by the hand of the broader community of users and developers forum.image.sc/

Image registration by feature extraction and matching across serial sections, from Saalfeld et al. 2012 Nature MethodsExample screenshot of LabKit, a plugin for image segmentation using machine learning, which needs but a handful of examples for training a random forest classifier.Example screenshot of the BigStitcher plugin for Fiji, showing many 3D image tiles stitched together.

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