@pchestek That's bizarre. Thousands of papers using pirated Photoshop for adjusting confocal and gel images for brightness and contrast would have to retracted – from prior to the subscription model of modern Photoshop.
(If you ever want to adjust B&C on an image, just use free open source software #FijiSc instead: https://fiji.sc )
This is a FIJI plugin that can analyze branched structures in a broad range of settings. They started with Microglia, but apparently it's broadly applicable (also works with neurons and even corals). Looks useful for analyzing 2D images.
AutoMorFi: Automated Whole-image Morphometry in Fiji/ImageJ for Diverse Image Analysis Needs
Bouadi ... Tuan Leng Tay, preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.07.26.605357v1.full
True as always that the way to make software run faster is to make it do less operations. After all, CPUs can only execute a fixed number of operations per unit of time.
Here, I tweaked code for serial section registration that drops execution time from 27 seconds to 100 milliseconds: a 270x speed up.
All it had to do is to search for matching SIFT features in one image only within a predetermined radius centered on one SIFT feature in another image. Extremely effective for when e.g., the maximum translation is known.
The matching code using a KDTree:
https://github.com/acardona/scripts/blob/master/java/asm/my/PointMatchesFast.java#L56
The test script:
https://github.com/acardona/scripts/blob/dev/python/imagej/FIBSEM/tests/test_matchNearbyFeatures.py
Online course on "Scientific Image Editing and Figure Creation" using open source software #FijiSc and #Inkscape.
By BioVoxxel via Zoom, on:
Thu 27 Jun 2024 09:00 - Fri 28 Jun 2024 15:30 CEST
Register at: https://www.tickettailor.com/events/biovoxxel/1198561
Details: https://www.biovoxxel.de/workshops/scientific-image-editing-and-figure-creation/
To non-faculty for sure. My first move would be to expand funding for PhD students: attract many, and with a good salary to bias the choice away from industry.
It's so cheap to support research work that may very well end up saving millions across the board, e.g., #FijiSc software to name just one close to me: https://albert.rierol.net/tell/20160601_Unintended_consequences_of_untimely_research.html
Image registration for light-microscopy at petabyte scale, an update of the #BigSticher for #FijiSc by @preibischs
https://github.com/JaneliaSciComp/BigStitcher-Spark
Ready for expansion microscopy #ExM approaches to mapping neural circuits and more.
There's an MRC 16-bit image file format reader here for #FijiSc: https://github.com/fiji/IO/blob/master/src/main/java/sc/fiji/io/Open_MRC_Leginon.java
The header includes MRC format details for documentation.
I wrote it.
Albert Cardona
nKiaru
Moritz Negwer
