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#ImageAnalysis

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Karsten Schmidt

To avoid a massive OpenCV dependency for a current project I'm involved in, I ended up porting my own homemade, naive optical flow code from 2008 and just released it as a new package. Originally this was written for a gestural UI system for Nokia retail stores (prior to the Microsoft takeover), the package readme contains another short video showing the flow field being utilized to rotate a 3D cube:

thi.ng/pixel-flow

I've also created a small new example project for testing with either webcam or videos:

demo.thi.ng/umbrella/optical-f

GIF
#ThingUmbrella#OpticalFlow#ImageAnalysis
Public
ResearchBuzz: Firehose

Baylor College of Medicine: New open-source platform supports large imaging data analysis. “A new open-source image analysis platform, developed by researchers at Baylor College of Medicine, Texas A&M University and the University of Houston, will now provide researchers with a powerful tool to analyze these large datasets in a computational resource efficient way, while including evaluation […]

https://rbfirehose.com/2024/12/12/baylor-college-of-medicine-new-open-source-platform-supports-large-imaging-data-analysis/

ResearchBuzz: Firehose | Individual posts from ResearchBuzz · Baylor College of Medicine: New open-source platform supports large imaging data analysis | ResearchBuzz: Firehose
More from ResearchBuzz: Firehose
#bigdata#dataanalysis#ImageAnalysis
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💧🌏 Greg Cocks

Alluvial Fan Surfaces And An Age-Related Stability For Cultural Resource Preservation: Nevada Test And Training Range, Nellis Air Force Base, Nevada, USA
--
doi.org/10.1016/j.jasrep.2015. <-- 2015 shared paper
--
[during a presentation recently, I was reminded of this 2015 paper’s content today (on which I was a co-author), back when papers wanted B&W images; I wonder how we might have proceeded now, with AI / Machine Learning…]
#GIS #spatial #mapping #Nevada #USA #military #NellisAFB #NAFB #NTTR #archaeology #spatialanalysis #spatiotemporal #corrleation #basinandrange #geomorphology #sediment #alluvialfans #sheetwash #eolian #erosion #deposition #bioturbation #varnish #desert #desertvarnish #age #dating #corrleation #airforce #indigeneous #sampling #cosmogenic #10Be #insitu #StonewallFlat #fans #water #hydrology #arid #imageanalysis #CulturalResource #Preservation

chart - correlation - alluvial fan average colour (as a grayscale) vs. analytical sampling age (years)
photos - alluvial fan surfaces and sampling locations
photo - scanned cover - 9th International Conference on Military Geoscience
photo - view of Stonewall Flats, Nevada, USA
Public
Moritz Negwer

Very excited that our whole-mouse-brain analysis pipeline - DELiVR - is published now at Nature Methods. With DELiVR, we built an open-source, easy-to-use pipeline for analyzing image stacks from cleared mouse brains.

Paper: nature.com/articles/s41592-024
Code: github.com/erturklab/delivr_cf
Docker containers, test dataset, handbook: discotechnologies.org/DELiVR/

Fig. 1 about DELiVR: Step 1: Tissue clearing, light-sheet microscopy Step 2: Generate custom training data in VR Step 3: run the analysis pipeline with the custom-trained deep-learning model inside the dockerized DELiVR pipeline
#neuroscience#tissueclearing#lightsheet
Public
Taffer 🇨🇦 :godot:

I found this really great app for identifying duplicate images, Czkawka: github.com/qarmin/czkawka

It does a bunch of other things (finding incorrect file extensions, finding broken files, etc.) and is ridiculously fast.

I wanted to write it down because I can never remember the name (Polish for "hiccup")!

GitHubGitHub - qarmin/czkawka: Multi functional app to find duplicates, empty folders, similar images etc.Multi functional app to find duplicates, empty folders, similar images etc. - qarmin/czkawka
#czkawka#imageanalysis#duplicate
Public
Virgile Andreani

@napari (a @NumFOCUS sponsored project) is a package I didn't know I needed, but which I can't live without anymore.
Super useful to visualize N-dimensional microscopy images (x, y, z, t, channel, scene).
I use it as a standalone viewer to visualize microscope images, but also during debugging, napari.imshow(image_array) spawns the viewer and this is so much more convenient than matplotlib!
There seems to be a healthy ecosystem of plugins too :)

The napari image viewer. On the left, some control boxes to combine image channels and tune contrast, gamma, colors and opacity. On the right, a list of 25 different scenes (microscope positions). On the bottom, a slider to select a timepoint. In the middle, a combined image with one visible channel and two fluorescence channels. The image is of a "mothermachine": a microfluidics device growing bacteria in channels open on one end only, so that growing bacteria are pushed outside of the channel and the "mother" cell remains in place at the top during all the experiment.
#Python#ImageAnalysis#Microscopy
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Karsten Schmidt

New #ThingUmbrella example (#147): Computing the RGB waveform[1] of an image using slit scanning & column-based histograms via thi.ng/pixel & thi.ng/transducers.

Demo (images are only processed locally on your own device):
demo.thi.ng/umbrella/pixel-wav

Source code:
github.com/thi-ng/umbrella/blo

This is by far not the fastest way to compute this, but it explains the principle approach more clearly. Almost exactly 13 years ago (to the day), I used the same with Java and my toxiclibs to transform images, driving altogether 768 granular oscillators to create super complex, constantly morphing drone sounds. Some selected audio snippets & images are here:

soundcloud.com/toxi/sets/granu
flickr.com/photos/toxi/sets/72

[1] It's called "waveform scope" in Adobe Premiere, even though the term is misleading...

RGB waveform of an example image, showing the complex signal graphs of the superimposed red, green and blue color channels of the image
#ImageProcessing#ImageAnalysis#Audio
Public
Patrick Martin

I might as well have make a pinned post.

We published Vesalius a tool that uses Image analysis methods to analyze spatial-omics data.

A new version will be coming soon that will include multimodal analysis and alignment!

GitHub: patrickcnmartin.github.io/Vesa

MSB: embopress.org/doi/full/10.1525

patrickcnmartin.github.ioVesaliusSpatial Transcriptomic Analysis using Image Analysis
#SpatialTranscriptomics#ImageAnalysis
Public
Virgile Andreani

I think people doing #ImageAnalysis and #microscopy should know about github.com/shssoichiro/oxipng

It is a lossless image optimization tool written in #rust. It rewrites the contents of an image to store it more efficiently, while maintaining exact pixel values.

One of my datasets went from 379 MiB to 162 MiB, a 57% reduction in size (it is even ~100 MiB smaller than the *zip archive* of the original dataset). It downloads faster, it reads faster, and the optimization was done in under 3 minutes.

GitHubGitHub - shssoichiro/oxipng: Multithreaded PNG optimizer written in RustMultithreaded PNG optimizer written in Rust. Contribute to shssoichiro/oxipng development by creating an account on GitHub.
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