@markmccaughrean

May I suggest #FijiSc https://fiji.sc which is a free and open source image processing software. Handling very large images should not be an issue. We handle volumes of many terabytes with it. Can open and write pretty much any file format imaginable, including raw, and offers a huge amount of image filters.

@quantixed Coincidentally, this year the #FijiSc software paper’s citations plateaued, after 10 years of growth (published in 2012 https://www.nature.com/articles/nmeth.2019 ), as if there weren’t any more labs that could start to cite it. Knowing the size of biology academia would be interesting.

@philiphubbard Have you tried Benjamin Schmid's 3D animation and rendering language, #3DScript, for #FijiSc:
https://bene51.github.io/3Dscript/

It's really not hard and surprisingly capable.

There's also a paper about it: https://www.nature.com/articles/s41592-019-0359-1

#ImageProcessing #3D

DeepImageJ 3.0 released—a user-friendly #FijiSc plugin that enables the use of a variety of pre-trained neural networks from the #BioimageModelZoo. Works with small and also very large images thanks to #ImgLib2.

https://deepimagej.github.io/

#DeepImageJ #PyTorch #TensorFlow #ImageJ #ImageProcessing

@ftrain Check out the open source Fiji image processing software https://fiji.sc and the image processing forum https://forum.image.sc

#FijiSc #ImageProcessing

Turns out, this is the result of an artifact: I had transform the images using integer coordinates rather than subpixel floating-point coordinates – my error. Hence these neatly drawn black spaces with sharp boundaries. The scripts have been corrected now; if you want to deliberately recreate this, for artistic purposes, then check the post: https://forum.image.sc/t/any-advice-on-making-a-thin-plate-spline-transform-more-precise/79595/3
#FijiSc

The underlying source code is here, if you want to try registering pairs of images with a non-linear transformation such as a thin-plate spline, on the bases of blockmatching features:

https://github.com/acardona/scripts/blob/master/python/imagej/examples/blockmatching_elastic_registration_X-ray.py

#FijiSc #jython #ImageProcessing #java

Every time I need to run an image processing task, the open source software #FijiSc delivers.

The javadocs are up to date https://javadoc.scijava.org/ , the libraries just work – particularly #ImgLib2 https://imagej.net/libs/imglib2/

And the examples of my own tutorial https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/ written in python 2.7 for the #JVM (#jython), despite some being a decade old, they all just work. Grateful every day for the outstanding backwards compatibility plus the new plugins and libraries that continue to grow https://fiji.sc

Many thanks to the many, many developers and maintainers, particularly Curtis Rueden, who is presently cutting out a new release: 2.11.0 https://forum.image.sc/t/plugin-maintainers-can-you-test-fiji-2-11-0/78852/18

#ImageProcessing

@hynek Same here—my best online posts are notes to future self, for e.g., image processing code snippets I don’t want to relearn. Here, some in #jython driving #FijiSc’s #java libraries to register images, transform N-dimensional images, visualise them in 2d/3d/4d, make GUIs, and more: https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial I hear many found these useful.

@florianjug @humantechnopole @AI4Life

Much envy, wish I was there. Been wanting to bring deep learning to some old corners of #FijiSc

@markkitti Wonderful. Is anyone going to test out deeplearning4j and how to use it from the Weka library, and maybe add a working example for #FijiSc's LabKit? Would be so useful to have this documented.

@alexwild @stevenbodzin Agree stacking is great in principle and often poor in practice. In my limited experience, stacking works best with great illumination (full sun, given no light equipment budget) and very short exposure times, and when managed directly by the camera as a brief burst (my Olympus TG-6 handles this somewhat well).
Ages ago I used #ImageJ’s Extended Depth of Field plugin http://bigwww.epfl.ch/demo/edf/index.html
#photography #FijiSc

@markkitti @HHMI Great to hear about the support for developing #imglib2 from #HHMI and #CZI! Tobias Pietzsch has made outstanding contributions to #imglib2 and #FijiSc in general, and now this support means he will have the means to continue to do so. Excellent!

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.

#java #python #kotlin #groovy

#TrakEM2 runs as a plugin of #FijiSc https://fiji.sc/ and in fact motivated the creation of the #FijiSc software in the first place, to manage its many dependencies and facilitate distribution to the broader #neuroscience community.

#TrakEM2 was founded in 2005, when TB-sized datasets were rare and considered large. Largest dataset I've successfully managed with #TrakEM2 was ~16 TB. For larger volumes see #CATMAID.

For 3D visualization #TrakEM2 uses the 3D Viewer https://imagej.net/plugins/3d-viewer/

@trinsec yeah let's do some #tootorials ! I might make threads about #FijiSc #bioimageanalysis #microscopy or #diy in the future! Anything like this ThreadReader yet for the fediverse?

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.
#java #python #kotlin #groovy

@engineeringjoy @Russpoldrack @weinberz @SherlockpHolmes @PracheeAC Welcome fellow #ImageJ -er. Curious about Ca2+ analysis: does it run within ImageJ (or #FijiSc?) and if so which plugin do you use?

@thor @riedl The academic world has a history of using open source software… and of creating it. My own: #FijiSc #TrakEM2 #CATMAID: https://qoto.org/@albertcardona/109269348386409802

@somedonkey Beautiful!

By the way this reminded me there's an upcoming paper by J-Y Tinevez and Pavel Tomancak on the open source software Mastodon (they are going to have to find a different hashtag) for #FijiSc that would benefit so much from your beautiful illustrations: https://github.com/mastodon-sc/mastodon

(The Mastodon cell tracking software is an evolution of their former MaMuT software https://imagej.net/plugins/mamut/index )