Eugene Katrukha 🇺🇦
@ekatrukha.bsky.social
Biophysics, cytoskeleton and self-disorganization
Pinned
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
forum.image.sc
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
Reposted by Eugene Katrukha 🇺🇦
ahah IT WORKS look it's a C² dual quaternion B-spline!!
this is interpolating *poses* in dual quaternion form, coupling position and rotation, instead of treating them independently (this is a really neat thing!!)
this is interpolating *poses* in dual quaternion form, coupling position and rotation, instead of treating them independently (this is a really neat thing!!)
November 26, 2025 at 3:10 AM
ahah IT WORKS look it's a C² dual quaternion B-spline!!
this is interpolating *poses* in dual quaternion form, coupling position and rotation, instead of treating them independently (this is a really neat thing!!)
this is interpolating *poses* in dual quaternion form, coupling position and rotation, instead of treating them independently (this is a really neat thing!!)
Reposted by Eugene Katrukha 🇺🇦
In our new #Preprint, we pilot a revolutionary new idea: no supplemental data (it has 21 figures, though):
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
www.biorxiv.org/content/10.1...
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
www.biorxiv.org/content/10.1...
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
We have previously shown that the calcium sensing receptor (CaSR) activates different G proteins and second messengers in single cells, and that GPCR and G protein-mediated ERK activity can be highly ...
www.biorxiv.org
November 24, 2025 at 8:29 AM
In our new #Preprint, we pilot a revolutionary new idea: no supplemental data (it has 21 figures, though):
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
www.biorxiv.org/content/10.1...
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
www.biorxiv.org/content/10.1...
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).
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
forum.image.sc
November 21, 2025 at 9:29 AM
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
Python notebook from a two year old paper:
Oh, no, I cannot run, there is a slight mismatch of a logging library.
ImageJ plugin from 2001 running on Quantum Java 51 in 2078:
Your 100 petabyte temporal hologram was successfully thresholded.
Oh, no, I cannot run, there is a slight mismatch of a logging library.
ImageJ plugin from 2001 running on Quantum Java 51 in 2078:
Your 100 petabyte temporal hologram was successfully thresholded.
November 20, 2025 at 5:42 PM
Python notebook from a two year old paper:
Oh, no, I cannot run, there is a slight mismatch of a logging library.
ImageJ plugin from 2001 running on Quantum Java 51 in 2078:
Your 100 petabyte temporal hologram was successfully thresholded.
Oh, no, I cannot run, there is a slight mismatch of a logging library.
ImageJ plugin from 2001 running on Quantum Java 51 in 2078:
Your 100 petabyte temporal hologram was successfully thresholded.
Reposted by Eugene Katrukha 🇺🇦
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
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)
Reposted by Eugene Katrukha 🇺🇦
Reposted by Eugene Katrukha 🇺🇦
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
November 12, 2025 at 2:41 AM
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
Reposted by Eugene Katrukha 🇺🇦
A game changer in our hands... www.nature.com/articles/s41...
Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods
u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...
www.nature.com
November 11, 2025 at 6:48 PM
A game changer in our hands... www.nature.com/articles/s41...
Reposted by Eugene Katrukha 🇺🇦
🔬🍀
A timelapse movie (unpublished data) from the lab.
In the movie, the nucleus is moving towards the base of the polarized root hair cell.
A timelapse movie (unpublished data) from the lab.
In the movie, the nucleus is moving towards the base of the polarized root hair cell.
November 11, 2025 at 6:01 PM
🔬🍀
A timelapse movie (unpublished data) from the lab.
In the movie, the nucleus is moving towards the base of the polarized root hair cell.
A timelapse movie (unpublished data) from the lab.
In the movie, the nucleus is moving towards the base of the polarized root hair cell.
Reposted by Eugene Katrukha 🇺🇦
I am beyond excited to share that my postdoc project @szndohrn.bsky.social and the @arnonelab.bsky.social is now available in #ScienceAdvances @science.org. www.science.org/doi/10.1126/...
November 5, 2025 at 7:02 PM
I am beyond excited to share that my postdoc project @szndohrn.bsky.social and the @arnonelab.bsky.social is now available in #ScienceAdvances @science.org. www.science.org/doi/10.1126/...
Reposted by Eugene Katrukha 🇺🇦
HL60 cells take on so many fun shapes as they migrate! This #InsightFromImaging data features cells prepared by Leanna and imaged on the @aicjanelia.bsky.social LLSM by @cmhobson.bsky.social
November 4, 2025 at 10:36 PM
HL60 cells take on so many fun shapes as they migrate! This #InsightFromImaging data features cells prepared by Leanna and imaged on the @aicjanelia.bsky.social LLSM by @cmhobson.bsky.social
Reposted by Eugene Katrukha 🇺🇦
"Neurons are highly polarized cells"
What other seemingly obligatory phrases do you notice in neuro papers?
November 4, 2025 at 6:32 PM
"Neurons are highly polarized cells"
Reposted by Eugene Katrukha 🇺🇦
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
Adventures in Code VII: getting started with napari – quantixed
quantixed.org
November 4, 2025 at 10:00 AM
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
Reposted by Eugene Katrukha 🇺🇦
We are planning the build of a light sheet setup and are considering a Powell lens to generate the sheet.
I've not been able to find a discussion of the pros and cons in literature, so if you ever used a Powell lens or have considered using one in your setup, I would love to hear your opinion. THX!
I've not been able to find a discussion of the pros and cons in literature, so if you ever used a Powell lens or have considered using one in your setup, I would love to hear your opinion. THX!
November 3, 2025 at 12:43 PM
We are planning the build of a light sheet setup and are considering a Powell lens to generate the sheet.
I've not been able to find a discussion of the pros and cons in literature, so if you ever used a Powell lens or have considered using one in your setup, I would love to hear your opinion. THX!
I've not been able to find a discussion of the pros and cons in literature, so if you ever used a Powell lens or have considered using one in your setup, I would love to hear your opinion. THX!
Reposted by Eugene Katrukha 🇺🇦
Exciting day for the lab: our 1rst paper is officially out in @currentbiology.bsky.social 🥳 Wonderful collaboration wt @gautamdey.bsky.social showing how Cryo-ExM achieves consistent immunostaining in diverse diatoms, from the lab and the natural environment 1/n
#ProtistsOnSky
tinyurl.com/2zxaund7
#ProtistsOnSky
tinyurl.com/2zxaund7
October 31, 2025 at 3:27 PM
Exciting day for the lab: our 1rst paper is officially out in @currentbiology.bsky.social 🥳 Wonderful collaboration wt @gautamdey.bsky.social showing how Cryo-ExM achieves consistent immunostaining in diverse diatoms, from the lab and the natural environment 1/n
#ProtistsOnSky
tinyurl.com/2zxaund7
#ProtistsOnSky
tinyurl.com/2zxaund7
Reposted by Eugene Katrukha 🇺🇦
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
October 31, 2025 at 2:42 PM
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
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...
Reposted by Eugene Katrukha 🇺🇦
Tracking has always been at the ❤️ of the scientific method, from planetary motion to single particles.
Weiqing’s thesis intro on tracking was so beautiful we turned it into a perspective in JCP who then selected it as a #Scilight.
Take a look! 😊
www.aip.org/scilights/tr...
Weiqing’s thesis intro on tracking was so beautiful we turned it into a perspective in JCP who then selected it as a #Scilight.
Take a look! 😊
www.aip.org/scilights/tr...
Tracing fluorescence tracking’s past, present, and future
Artificial intelligence and parallel computing could refine studies of the movement of single molecules inside cells.
www.aip.org
October 30, 2025 at 11:19 PM
Tracking has always been at the ❤️ of the scientific method, from planetary motion to single particles.
Weiqing’s thesis intro on tracking was so beautiful we turned it into a perspective in JCP who then selected it as a #Scilight.
Take a look! 😊
www.aip.org/scilights/tr...
Weiqing’s thesis intro on tracking was so beautiful we turned it into a perspective in JCP who then selected it as a #Scilight.
Take a look! 😊
www.aip.org/scilights/tr...
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.
Reposted by Eugene Katrukha 🇺🇦
PAPER OUT ✨ What if you could use your microscope as a 3D printer? Prototype microfluidics in-house, <5$ in material costs per chip. From idea to experiment within a day. Now published in Lab-on-a-Chip (open-access): doi.org/10.1039/D5LC...
July 16, 2025 at 11:51 AM
PAPER OUT ✨ What if you could use your microscope as a 3D printer? Prototype microfluidics in-house, <5$ in material costs per chip. From idea to experiment within a day. Now published in Lab-on-a-Chip (open-access): doi.org/10.1039/D5LC...
Reposted by Eugene Katrukha 🇺🇦
The #mesoSPIM symposium really opened my eyes to the power of open source hardware. I've highlighted some of the surprising outcomes in a new blog post:
How Open Source Microscopy is Solving the Funding Crisis: Insights from the mesoSPIM 10-Year Symposium
www.syglass.io/blog/how-ope...
How Open Source Microscopy is Solving the Funding Crisis: Insights from the mesoSPIM 10-Year Symposium
www.syglass.io/blog/how-ope...
October 23, 2025 at 4:17 PM
The #mesoSPIM symposium really opened my eyes to the power of open source hardware. I've highlighted some of the surprising outcomes in a new blog post:
How Open Source Microscopy is Solving the Funding Crisis: Insights from the mesoSPIM 10-Year Symposium
www.syglass.io/blog/how-ope...
How Open Source Microscopy is Solving the Funding Crisis: Insights from the mesoSPIM 10-Year Symposium
www.syglass.io/blog/how-ope...
Reposted by Eugene Katrukha 🇺🇦
for #FluorescenceFriday : is your ExM sample too large to be imaged with high NA objectives? VIPS it! Very clever way to tackle one of the biggest challenge in large volumetric ExM www.science.org/doi/10.1126/...
Mesoscale volumetric fluorescence imaging at nanoscale resolution by photochemical sectioning
Optical nanoscopy of intact biological specimens has been transformed by recent advancements in hydrogel-based tissue clearing and expansion, enabling the imaging of cellular and subcellular structure...
www.science.org
October 17, 2025 at 12:29 PM
for #FluorescenceFriday : is your ExM sample too large to be imaged with high NA objectives? VIPS it! Very clever way to tackle one of the biggest challenge in large volumetric ExM www.science.org/doi/10.1126/...
Reposted by Eugene Katrukha 🇺🇦
We are looking for an #AIEngineer to help build protein language models that capture evolutionary constraints with @matsen.bsky.social and @jbloomlab.bsky.social at #AI@HHMI @hhmijanelia.bsky.social
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
AI Engineer - Evolutionary Protein Language Models
Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. Intro: AI@HHMI: HHMI is investing $500 million over the next 10 years ...
hhmi.wd1.myworkdayjobs.com
September 18, 2025 at 4:50 PM
We are looking for an #AIEngineer to help build protein language models that capture evolutionary constraints with @matsen.bsky.social and @jbloomlab.bsky.social at #AI@HHMI @hhmijanelia.bsky.social
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com/en-US/Extern...