Am I being dense or is there really no way to get the path of the currently running ijm macro in #fiji #imageJ

getInfo("macro.filepath") returns the path of the check for updates macro. Not my currently running macro.

Ah, feeling nostalgic, my former colleague became the new poster child for image tests in computer vision: a test image built in #ImageJ # FIJI

(I am making figure to explain perceptionally uniform #color scales...)
#NewLenna #Lenna #DataVis

Fighting #ImageJ today. It's losing greyscale calibration when I crop a section from a larger image.

That said in typing this I think I worked out how to fix it. Thank you all for being my rubberduck.

From @nvladimus : "We have opened the #mesoSPIM official User Forum" at https://forum.image.sc/tag/mesospim alongside #Fiji #ImageJ #ilastik #BiaPy #napari #DeepLabCut and many other open source softwares for bioimage informatics.

How would a signal look like from our micro-ring resonator #MRR #biosensor?

We observe a spectrum in a wavelength range around 1.55 µm by coupling the laser radiation into an array of five MRRs, see bottom figure. It is notable that each MRR has a curved triangular shape of different size this causes the resonance peak of each MRR to occur at different positions in the spectrum.

In the spectrum range investigated, we observed four groups of resonance peaks corresponding to four standing waves occurring to each of the five rings.

Determining the perimeter of the ring was challenging. I used #ImageJ to draw a polygon that approximated the triangular shape and measured the perimeter. Then, with the use of the formulas obtained from P. Steglich, et al(https://ieeexplore.ieee.org/abstract/document/9568878), it was possible to determine the effective refractive index nff and the order m of the standing wave.

#microelectronic #bioelectronic

Light-Sheet Image Analysis Workshop 2026

The Light-Sheet Image Analysis Workshop is a five-day intensive course that will take place in Santiago, Chile, from January 5–9, 2026, designed for students and researchers who wish to gain foundational skills in the processing and analysis of light-sheet microscopy imaging data.

The application deadline has been extended until August 8, 2025! The workshop is free to attend and travel fellowships are available. Learn more and apply here:

https://lightsheetchile.cl/light-sheet-image-analysis-workshop-2026-2/

—
URL: https://brunovellutini.com/posts/light-sheet-image-analysis-workshop-2026/

#event #imageProcessing #imagej #lightsheet #microscopy

@stephenturner.us

This is great spatially-resolved transcriptomics by the R/Bioconductor package visiumStitched, which facilitates stitching the images together with Fiji (ImageJ). 🦾

#rstats #Fiji #ImageJ #Bioconductor #visiumStitched

Tried the same with a more realistic 3D stack from the #ImageJ sample library.#Cellpose runs fast and segments very well out of the box.#CellSeg3D takes considerably longer and seems to segment decently, but I couldn’t get a proper instance #segmentation in the post-processing step (which is recommended as part of its workflow). However, #CellSeg3D looks very promising — just needs some more time and parameter exploration, I guess.

I’d recommend giving it a try 👌

I promised myself a while back that I wouldn't write any more #ImageJ Macro code. When I made this promise I forgot about all the scripts that we have in use. “Oh, this one just needs a few tweaks and then it can be used in another project." And here I am again in ijm hell!

#AdventuresInCode #LifeOfPI

Any image editing experts here? Colour variation is partially due to moisture and does not really bother me so much. But the variation in brightness annoys me. Any ideas how to tackle this? Histogram equalisation did not help much. Any suggestions are welcome! #ImageJ

RE: https://bsky.app/profile/did:plc:ixbyd26kgncs6rafjxvoo4l7/post/3lixe5fbf7s2l

Tips from the Blog XVII: better Process Folder template in Fiji

https://quantixed.org/2025/02/16/tips-from-the-blog-xvii-better-process-folder-template-in-fiji/

#AdventuresInCode #computing #FIJI #ImageJ #tftb

🌟 🌈 🔭

Aprovechando un poco el buen tiempo por acá.

🌌 🥰
Sacando espectros de estrellas, teniendo como plato fuerte estrellas en Orión.

En este caso, el tercer espectro extraído: Betelgeuse.

🐧
Usando #Kstars en la captura, @siril.org para el apilado #ImageJ para graficar.

#SoftwareLibre

Am Zukunftstag hatte ich eine interessierte Besucherin hier im Labor.

Sie hat eine munzig kleine Spinne aus dem Feuerholzstapel zuhause mitgenommen (der Hinterkörper der Spinne ist 1.7 mm dick).

Diese haben wir in etwas Schaumstoff eingebettet und dann auf unserem #Bruker #SkyScan 2214 aufgenommen (mit 3 um Pixelgrösse).
Dann haben wir die Tomographiedaten angeschaut und in #ImageJ an den Schnittbildern ein paar Dinge daran gemessen (deshalb wissen wir, das der Hinterkörper 1.7 mm dick ist).

Here's a small recursive image of the Fiji logo made in #ImageJ and #Fiji

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. #ImageJ
#Fiji
#BigDataViewer

Some people are just nuts. I love it.

See what this guy did with the #ImageJ
macro language.

https://www.reddit.com/r/ImageJ/comments/1gfbnkq/strange_fiji_macro_shows_weird_video_feed/

#µManager: #OpenSource software for control & #automation of #microscope #hardware:

-integrated with #ImageJ
-works with #Leica, #Nikon, #Olympus & #Zeiss

Web: https://micro-manager.org/
Github: https://github.com/micro-manager

#DIYbio #lab #instruments #MicroManager #microscopy #imaging

If I do a PR to fix this one-letter typo in #ImageJ is everybody going to think I have lost the plot.

#GitHub

When I search for documentation on ImageJ (the image processing library for Java) I get LOADS of hits about science image-processing software with the same name. I'm starting to think they might be the same thing. ARE they? Or am I confused? Are there two things called ImageJ?

#Software #Coding #ImageJ