Here's a #BIAToolTip for the weekend! As Tuco says in the movie, there are two kinds of processing for image quantification in the world - there's processing for intensity measurement, and there's processing for segmentation.

Know which way you'll go before choosing filters!

#bioimageanalysis

A screenshot showing the use of the Windows ColourSimulatons app to quickly check color blind friendly display and color usage in images. It shows one image of fluorescently stained cells while combining red, green and blue colors and another one using cyan, yellow and magenta together with the apps sliding window that simulates the color blind vision on screen. Additionally it displays the pop-up menu for the tool.

#BIAToolTip No.15

On Windows there is the ColourSimulator App which allows you to simulate on your screen with a slidable window to inspect design or images to check if those are inclusive for color deficient vision.
The #biovoxxel LUT Channels Tool provides a related functionality.

color inspector UI

color inspector example including stain separation from a histological image with blue nuclei and brownish DAB staining

#BIAToolTip No.14
The Color Inspector 3D is a super useful tool to visualize color distribution in different color spaces for RGB images and can facilitate non-quantitative stain segmentation e.g. in IHC stainings. Available in #ImageJ and #Fiji
#bioimageanalysis

Btw., no time for a #BIAToolTip today. So, I cheat,... the book will be my tip of the day (even though not read yet... no risk, no fun)

clij.github.io GPU accelerated image processing for everyone

#BIAToolTip No.13
A Must-Know: the amazing CLIJ2 library from @haesleinhuepf.bsky.social and its IJ macro extensions make image processing and analyses of 2D/3D images on the GPU a breeze and super flexible. Huge function repository, a very neat clij2 assistant and super easy to macro record.

Western blot analysis information Dear all, Since once in a while the topic semi-quantitative Western blot analysis pops up and many people in biological sciences who do Western blots or gels are into that, I wanted to share some inf...

#BIAToolTip No.12
I wanted to highlight information regarding Western Blot analysis which is often performed in questionable ways. If you google for tutorials online many instructions you find are often quite (!) incorrect 🤯. Here some literature links and a suitable tool: GelAnalyzer

#BIAToolTip No.11 (actually more a processing tip)

A variance filter (or edge detection) can facilitate object segmentation in DIC or brightfield images. In the example below it even outperforms cellpose (even after various parameter tunings). Worth a test if custom model training is not feasible.

#BIAToolTip No.10 (SPECIAL)

NEW release of #biovoxxel Figure Tools v4.0.0.

Now, interactive merge images can be created as mentioned here: bsky.app/profile/biov...

All channel combinations can be checked in the resulting SVG files when opened in the browser.

#BIAToolTip No.9
Catching the ball from @guijacquemet.bsky.social and his NeuroCyto LUTs post. The LUT Channels Tool from the #biovoxxel Figure Tools can be equipped with any LUTs in the IJ lut folder or your favorite LUTs in a subfolder. Comes with all IJ channel functions and a color blind test.

#BIAToolTip No.8
In addition to my last [#BIAToolTip No.8](bsky.app/profile/biov...) the Tubness Filter in ImageJ is an underestimated feature. It helps preprocessing line-like structures in 2D/3D for consecutive segmentation/tracing. It can also serve for object separation (coming up).

Ridge Detection The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...

#BIAToolTip No.7

The Ridge Detection plugin from @thorstenwagner.bsky.social is really nice tool gem to automatically detect line-like structures in regular sized images in 2D/3D.
Even though, not actively maintained anymore, it runs stable and does what it should.

For today's #BIATooloftheday #BIAToolTip, a great way to dip your toe into powerful analysis tools. There are few things as zennish as watching a huge batch of open images disappear as a simple processing macro zips through the stack. I know batch mode goes faster but it's nice to watch. #Fiji

#BIAToolTip No.6
Object or label separation, especially in 3D, are not trivial but the Label Splitter from the #biovoxxel 3D box if offering several algorithms that reduce bleed-over into neighboring objects.

Doc: biovoxxel.github.io/bv3dbox/#lab...

Video: youtu.be/H-NWVafWLfo?...

#BIAToolTip No.5
3D Object segmentation mostly involves object separation.
Both works often better if you have isotropic voxels!
"Make 3D Image Isotropic" or "Make Voxel Isotropic" from the #biovoxxel 3D box does this straight forward.

forum.image.sc/t/imagej-nuc...

Adjustable Watershed The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...

#BIAToolTip No.4
Object separation in 2D via the default watershed algorithm in IJ often suffers from over- or under-fragmentation.
The "Adjustable Watershed" from Michael Schmid is a nice and simple alternative to improve object separation after classical binarization.
imagej.net/plugins/adju...

GitHub - biovoxxel/BioVoxxel-Figure-Tools Contribute to biovoxxel/BioVoxxel-Figure-Tools development by creating an account on GitHub.

#BIAToolTip No.3
In this thread I will introduce several of the #biovoxxel figure tools for Fiji that allow you to prepare images for scientific figures in line with GSP and preserving image quality as well as data integrity 100%
github.com/biovoxxel/Bi...

In Fiji / ImageJ you can check it under Image › Color › Simulate Color Blindness or using the indicated button in the image below via the LUT channels tool from the #Biovoxxel Figure Tools which has much more to offer and I will feature this in the next #BIAToolTip post.

#BIAToolTip No.2
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.

In Fiji/ImageJ the shortcut ([Ctrl] +) [Shift] + [U] brings up the normally hidden Plugins › Utilities › Control Panel (by Cezar Tigaret) This gives quick access to the complete Fiji menu and specific panes you use often can be detached by simple dragging

#BIAToolTip No. 1
In Fiji/ImageJ the shortcut ([Ctrl] +) [Shift] + [U] brings up the normally hidden Plugins › Utilities › Control Panel (by Cezar Tigaret)
This gives quick access to the complete Fiji menu and specific panes you use often can be detached by simple dragging ⌨️

I got inspired by @guijacquemet.bsky.social's idea of making regular posts on #bioimageanalysis tools and tips under #BIATooloftheday. Will try to complement his suggestions with as little overlap as possible under #BIAToolTip with a focus on #Fiji and #ImageJ and friends.
In the hope it helps