Benedikt Wimmer
@bwmr.net
PostDoc at the Jacobs-Wegner lab in Stanford. Previously at the Medalia Lab (Zurich) and Chlanda lab (Heidelberg). Using cryo-ET and light microscopy to study bacteria and how they help and hurt us. #teamtomo
Thanks Marten! With pytom-match-pick, getting the ribosome average ready for the rendering was a breeze! :)
April 4, 2025 at 11:39 AM
Thanks Marten! With pytom-match-pick, getting the ribosome average ready for the rendering was a breeze! :)
(5/5)
It was a particular pleasure to work with a multi-disciplinary and international team on this project, from the University of Zurich, Ben-Gurion University in Beer-Sheva and the University of Greifswald!
It was a particular pleasure to work with a multi-disciplinary and international team on this project, from the University of Zurich, Ben-Gurion University in Beer-Sheva and the University of Greifswald!
April 3, 2025 at 12:41 PM
(5/5)
It was a particular pleasure to work with a multi-disciplinary and international team on this project, from the University of Zurich, Ben-Gurion University in Beer-Sheva and the University of Greifswald!
It was a particular pleasure to work with a multi-disciplinary and international team on this project, from the University of Zurich, Ben-Gurion University in Beer-Sheva and the University of Greifswald!
(4/5)
By combining in-situ #cryoet and #proteomics, we could assemble an integrative model, which illustrates the remarkable architecture of the amylosome - the complex that allows R. bromii to act as keystone degrader in the gut microbiome.
By combining in-situ #cryoet and #proteomics, we could assemble an integrative model, which illustrates the remarkable architecture of the amylosome - the complex that allows R. bromii to act as keystone degrader in the gut microbiome.
April 3, 2025 at 12:41 PM
(4/5)
By combining in-situ #cryoet and #proteomics, we could assemble an integrative model, which illustrates the remarkable architecture of the amylosome - the complex that allows R. bromii to act as keystone degrader in the gut microbiome.
By combining in-situ #cryoet and #proteomics, we could assemble an integrative model, which illustrates the remarkable architecture of the amylosome - the complex that allows R. bromii to act as keystone degrader in the gut microbiome.
(3/5)
We wanted to understand, why it makes such a complicated assembly, and found through structural and biochemical analysis that two key enzymes act synergistically if they are bound in amylosome-like complexes. #proteomics revealed that this complex is enriched when needed.
We wanted to understand, why it makes such a complicated assembly, and found through structural and biochemical analysis that two key enzymes act synergistically if they are bound in amylosome-like complexes. #proteomics revealed that this complex is enriched when needed.
April 3, 2025 at 12:41 PM
(3/5)
We wanted to understand, why it makes such a complicated assembly, and found through structural and biochemical analysis that two key enzymes act synergistically if they are bound in amylosome-like complexes. #proteomics revealed that this complex is enriched when needed.
We wanted to understand, why it makes such a complicated assembly, and found through structural and biochemical analysis that two key enzymes act synergistically if they are bound in amylosome-like complexes. #proteomics revealed that this complex is enriched when needed.
(2/5)
Our gut microbiome is essential for our health, and it relies on dietary fiber to thrive. The nutrients in dietary fiber, however, are very hard to access. Only few bacterial species manage to do so!
Our subject, R. bromii, is one of them - by using an extracellular assembly called amylosome.
Our gut microbiome is essential for our health, and it relies on dietary fiber to thrive. The nutrients in dietary fiber, however, are very hard to access. Only few bacterial species manage to do so!
Our subject, R. bromii, is one of them - by using an extracellular assembly called amylosome.
April 3, 2025 at 12:41 PM
(2/5)
Our gut microbiome is essential for our health, and it relies on dietary fiber to thrive. The nutrients in dietary fiber, however, are very hard to access. Only few bacterial species manage to do so!
Our subject, R. bromii, is one of them - by using an extracellular assembly called amylosome.
Our gut microbiome is essential for our health, and it relies on dietary fiber to thrive. The nutrients in dietary fiber, however, are very hard to access. Only few bacterial species manage to do so!
Our subject, R. bromii, is one of them - by using an extracellular assembly called amylosome.
You can find the plugin on napari-hub here: www.napari-hub.org/plugins/napa...
and the GitHub repository here: github.com/bwmr/napari-...
and the GitHub repository here: github.com/bwmr/napari-...
SegSelect - napari Plugin - Benedikt Wimmer
Select a connected component from a membrain-seg segmentation.
www.napari-hub.org
February 6, 2025 at 11:02 AM
You can find the plugin on napari-hub here: www.napari-hub.org/plugins/napa...
and the GitHub repository here: github.com/bwmr/napari-...
and the GitHub repository here: github.com/bwmr/napari-...
... which can then be written out as binary masks in the mrc format and visualized or used however you like:
February 6, 2025 at 11:02 AM
... which can then be written out as binary masks in the mrc format and visualized or used however you like:
... and allows you to easily create labels containing only the IDs of interest.
February 6, 2025 at 11:02 AM
... and allows you to easily create labels containing only the IDs of interest.
"napari-segselect" automatically opens the "*_segmented.mrc" files from membrain-seg as a label field...
February 6, 2025 at 11:02 AM
"napari-segselect" automatically opens the "*_segmented.mrc" files from membrain-seg as a label field...
If you want to split them up into individual segmentations, to assign different colors, or create masks for further processing, etc., membrain-seg has the flag "--store-connected-components", which assigns each connected volume a unique ID.
February 6, 2025 at 11:02 AM
If you want to split them up into individual segmentations, to assign different colors, or create masks for further processing, etc., membrain-seg has the flag "--store-connected-components", which assigns each connected volume a unique ID.