Eugene Katrukha 🇺🇦
@ekatrukha.bsky.social
Biophysics, cytoskeleton and self-disorganization
Trying "surface" render mode for volumetric (segmentation here) data for #BigVolumeBrowser (not released yet).
November 21, 2025 at 3:26 PM
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)
November 21, 2025 at 9:32 AM
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).
November 17, 2025 at 10:06 PM
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)
It was hard not to load our building and around it into #bigvolumebrowser (22 M points + Fire LUT for height)
November 17, 2025 at 4:38 PM
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)
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?
November 5, 2025 at 5:57 AM
What that a kiwi bird passing by?
Something like this?
In principle, it would be rarely used with a caption. And for icon, only cubes (square) should be enough.
In principle, it would be rarely used with a caption. And for icon, only cubes (square) should be enough.
November 4, 2025 at 9:46 AM
Something like this?
In principle, it would be rarely used with a caption. And for icon, only cubes (square) should be enough.
In principle, it would be rarely used with a caption. And for icon, only cubes (square) should be enough.
How a trick from flow cytometry can help colocalization visualization for microscopy forum.image.sc/t/cytofluoro...
October 31, 2025 at 10:32 AM
How a trick from flow cytometry can help colocalization visualization for microscopy forum.image.sc/t/cytofluoro...
Internet people, please help me to decide on the logo for #bigvolumebrowser, a multi-volume 3D viewer plugin for Fiji I'm working on. Please vote by replying with a number or liking one that was already mentioned. My favorites are 6, 7, 8 and 10 so far.
October 28, 2025 at 1:55 PM
Internet people, please help me to decide on the logo for #bigvolumebrowser, a multi-volume 3D viewer plugin for Fiji I'm working on. Please vote by replying with a number or liking one that was already mentioned. My favorites are 6, 7, 8 and 10 so far.
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
October 17, 2025 at 3:35 PM
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
October 10, 2025 at 11:06 AM
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).
October 10, 2025 at 10:39 AM
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
September 30, 2025 at 12:52 PM
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
Good morning, if you didn't sleep good (on top of a cupboard)
September 30, 2025 at 6:46 AM
Good morning, if you didn't sleep good (on top of a cupboard)
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).
September 26, 2025 at 1:20 PM
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...
September 24, 2025 at 12:05 PM
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.
September 19, 2025 at 10:38 AM
A cell finding its way through the matrix, imaged with @joycemeiri.bsky.social on LLS.
Nice, some MTs splaying to individual protofilaments upon bending with two optical traps.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 12, 2025 at 10:18 AM
Nice, some MTs splaying to individual protofilaments upon bending with two optical traps.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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)
September 5, 2025 at 3:48 PM
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)
September 5, 2025 at 3:43 PM
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)
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)
September 5, 2025 at 3:37 PM
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)
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)
SMLM quantification of microtubule fixation protocol. Looks like a classic extraction is the best
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
August 28, 2025 at 9:55 AM
SMLM quantification of microtubule fixation protocol. Looks like a classic extraction is the best
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
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
August 27, 2025 at 11:40 AM
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
Oh, nice, just found a paper from @joergenderlein.bsky.social and co on blind estimation of IRF for FLIM measurements pmc.ncbi.nlm.nih.gov/articles/PMC...
It should be useful!
It should be useful!
August 19, 2025 at 3:35 PM
Oh, nice, just found a paper from @joergenderlein.bsky.social and co on blind estimation of IRF for FLIM measurements pmc.ncbi.nlm.nih.gov/articles/PMC...
It should be useful!
It should be useful!
Last feature for #bigvolumebrowser before vacation:
"inverted" clipping
"inverted" clipping
July 31, 2025 at 9:53 AM
Last feature for #bigvolumebrowser before vacation:
"inverted" clipping
"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
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
July 28, 2025 at 9:10 PM
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
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