Trying "surface" render mode for volumetric (segmentation here) data for #BigVolumeBrowser (not released yet).

Manuals and code are at github repository + wiki link github.com/UU-cellbiolo... (2/2)

No, actually, our scan is better. Balconies are bad; it seems like LIDAR cannot reach the back wall (you can see trees behind the building).

Turns out, there are fully opened LIDAR point scans of the whole Netherlands surface available geotiles.nl With up to 25 cm.
It was hard not to load our building and around it into #bigvolumebrowser (22 M points + Fire LUT for height)

What that a kiwi bird passing by?

Hello dear diary, today I've added some minor features, like highlighting boxes and canvas selecting objects + manual transform mode. Small update, mucho trabajo, but it should be helpful for user experience #bigvolumebrowser

And z-depth color coding and opacity mapping to localization precision make 3D SMLM render more pretty

LUT color mapping for spots/particles rendering in #bigvolumeviewer is almost finished. The speed is mapped by color (middle) and color + spot size (right).

One step at a time, first just trying to verify the upload of the LUT texture to the GPU. So I mapped it to whatever (here on a spot shape). Looks weird, but I like those intermediate "debug" results. It seems to work; now I can implement a proper depth color-coding. #bigvolumebrowser

Back to work on #bigvolumebrowser, I've added the import of point clouds that change over time. The test data generation was a pleasant detour into the world of attractors (Thomas' cyclically symmetric is shown).

New release of #BigTrace plugin is out. Together with @aafkegros.bsky.social from Simone Köhler group we added a fully automatic tracing mode. + more macro functions and bug fixes github.com/ekatrukha/Bi...

A cell finding its way through the matrix, imaged with @joycemeiri.bsky.social on LLS.

We developed a workflow to detect and extract a hundred volumes of basal bodies (BB) from the cell surface. Since cilia are beating and BB appear pretty crooked, we straightened them and developed an alignment and averaging procedure. That allowed us to map their protein composition (3/N)

Using expansion microscopy, we re-examined MT organization and mapped PTMs in the human airway multiciliated cells during differentiation. Basal bodies seem to serve the role of main MTOCs (2/N)

Our new preprint is about the airway epithelium microtubule network, cilia, basal body protein composition, averaging of volumetric fluorescence data, and expansion microscopy.
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)

I rarely see the "depth of field effect" for 3D microscopy datasets rendering. Tried to implement it as a weekend project. Curious, if it can be useful #bigvolumebrowser

Last feature for #bigvolumebrowser before vacation:
"inverted" clipping

Interestingly, the (s)CMOS (+BSI) camera revolution of the last 5-6 years has also reached the field of high-speed cameras.
It seems that in 2020, their price was still around 150k for a max speed of ~2000 fps. These days, one can buy 50000 fps camera for just 60k. The videos are pretty amazing