Hi,
@haesleinhuepf.bsky.social
for image registration purposes I need to select matching landmarks from images.
Are you aware of a jupyter widget that can help with that?
I don't want to download all my images from my HPC.
@haesleinhuepf.bsky.social
for image registration purposes I need to select matching landmarks from images.
Are you aware of a jupyter widget that can help with that?
I don't want to download all my images from my HPC.
September 24, 2025 at 2:34 PM
Hi,
@haesleinhuepf.bsky.social
for image registration purposes I need to select matching landmarks from images.
Are you aware of a jupyter widget that can help with that?
I don't want to download all my images from my HPC.
@haesleinhuepf.bsky.social
for image registration purposes I need to select matching landmarks from images.
Are you aware of a jupyter widget that can help with that?
I don't want to download all my images from my HPC.
Hi @jef.works
there is interest in showcasing STalign in a big spatial tutorial.
However the current requirements.txt make it difficult to include.
Could you take a look at
github.com/JEFworks-Lab...
there is interest in showcasing STalign in a big spatial tutorial.
However the current requirements.txt make it difficult to include.
Could you take a look at
github.com/JEFworks-Lab...
September 2, 2025 at 4:10 PM
Hi @jef.works
there is interest in showcasing STalign in a big spatial tutorial.
However the current requirements.txt make it difficult to include.
Could you take a look at
github.com/JEFworks-Lab...
there is interest in showcasing STalign in a big spatial tutorial.
However the current requirements.txt make it difficult to include.
Could you take a look at
github.com/JEFworks-Lab...
Reposted by Methylrot
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
February 12, 2025 at 11:10 AM
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
Reposted by Methylrot
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.03.31.646342v1
https://www.biorxiv.org/content/10.1101/2025.03.31.646342v1
April 3, 2025 at 4:00 PM
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.03.31.646342v1
https://www.biorxiv.org/content/10.1101/2025.03.31.646342v1
Reposted by Methylrot
Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?
If so, you might this little project: github.com/rrwick/conda...
If so, you might this little project: github.com/rrwick/conda...
GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions
a simple tool for listing conda environments with descriptions - rrwick/condaenvlist
github.com
March 27, 2025 at 4:34 AM
Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?
If so, you might this little project: github.com/rrwick/conda...
If so, you might this little project: github.com/rrwick/conda...
Reposted by Methylrot
Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...!
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
https://www.nature.com/articles/s41592-025-02624-3🎉
March 18, 2025 at 3:40 PM
Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...!
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
Reposted by Methylrot
Reassuring news for PhD students everywhere. Extracts from Crick’s lab-book 1949-50:
March 7, 2025 at 8:32 AM
Reassuring news for PhD students everywhere. Extracts from Crick’s lab-book 1949-50:
Reposted by Methylrot
📦 Packaging Python apps just got easier! @rjai.me 's latest #QuansightLabs blog explores how napari's team reimagined installers, creating tools that benefit the entire scientific computing community. https://buff.ly/4jMCZxx 🔬 #OpenSourceInnovation
From napari to the world: how we generalized the `conda/constructor` stack for distributing Python applications
Our work for the napari project resulted in multiple beneficial side effects for the conda packaging ecosystem.
buff.ly
February 4, 2025 at 5:00 PM
📦 Packaging Python apps just got easier! @rjai.me 's latest #QuansightLabs blog explores how napari's team reimagined installers, creating tools that benefit the entire scientific computing community. https://buff.ly/4jMCZxx 🔬 #OpenSourceInnovation
Reposted by Methylrot
Reminder that @europepmc.org is a mirror of Pubmed with better search and that it indexes *all* bioRxiv preprints (as well as ResearchSquare), not just the ones funded by NIH like chauvinist Pubmed
I’m very scared to see what happens to PubMed
January 31, 2025 at 8:44 PM
Reminder that @europepmc.org is a mirror of Pubmed with better search and that it indexes *all* bioRxiv preprints (as well as ResearchSquare), not just the ones funded by NIH like chauvinist Pubmed
Reposted by Methylrot
a bit more #Severance data
please enjoy all analyses equally
👉 lucymcgowan.github.io/mdr-website/
and for my #rstats friends:
👉 lucymcgowan.github.io/mdr/
please enjoy all analyses equally
👉 lucymcgowan.github.io/mdr-website/
and for my #rstats friends:
👉 lucymcgowan.github.io/mdr/
January 31, 2025 at 2:54 PM
a bit more #Severance data
please enjoy all analyses equally
👉 lucymcgowan.github.io/mdr-website/
and for my #rstats friends:
👉 lucymcgowan.github.io/mdr/
please enjoy all analyses equally
👉 lucymcgowan.github.io/mdr-website/
and for my #rstats friends:
👉 lucymcgowan.github.io/mdr/
Hi,
@brukerspatial.bsky.social
In www.nature.com/articles/s41...
You presented a dataset with 980 RNAs and 108 proteins.
But on staging.nanostring.com/products/cos... I only find the RNA and a couple of protein markers for QC and segmentation.
Where can I find the rest of the protein data?
Ty!
@brukerspatial.bsky.social
In www.nature.com/articles/s41...
You presented a dataset with 980 RNAs and 108 proteins.
But on staging.nanostring.com/products/cos... I only find the RNA and a couple of protein markers for QC and segmentation.
Where can I find the rest of the protein data?
Ty!
January 20, 2025 at 10:13 PM
Hi,
@brukerspatial.bsky.social
In www.nature.com/articles/s41...
You presented a dataset with 980 RNAs and 108 proteins.
But on staging.nanostring.com/products/cos... I only find the RNA and a couple of protein markers for QC and segmentation.
Where can I find the rest of the protein data?
Ty!
@brukerspatial.bsky.social
In www.nature.com/articles/s41...
You presented a dataset with 980 RNAs and 108 proteins.
But on staging.nanostring.com/products/cos... I only find the RNA and a couple of protein markers for QC and segmentation.
Where can I find the rest of the protein data?
Ty!
Reposted by Methylrot
In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
December 12, 2024 at 11:24 AM
In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Reposted by Methylrot
Are you frustrated by how GitHub renders Jupyter notebooks? I have public service that renders GitHub notebooks with Quarto
nbsanity.com
It now works with gists!
nbsanity.com
It now works with gists!
December 7, 2024 at 7:42 PM
Are you frustrated by how GitHub renders Jupyter notebooks? I have public service that renders GitHub notebooks with Quarto
nbsanity.com
It now works with gists!
nbsanity.com
It now works with gists!
Reposted by Methylrot
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
www.nature.com
December 6, 2024 at 8:52 PM
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
Reposted by Methylrot
Excited to share a new algorithm that we have been working on over the last year.
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
December 5, 2024 at 4:31 PM
Excited to share a new algorithm that we have been working on over the last year.
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
Reposted by Methylrot
There are several gems in there (e.g., you should look at scores on embeddings or graphs of your single cell data! not just partition-based metrics), but also ..
December 5, 2024 at 12:52 PM
There are several gems in there (e.g., you should look at scores on embeddings or graphs of your single cell data! not just partition-based metrics), but also ..
Reposted by Methylrot
A little piece that's been in the works with former MSc, now PhD student, Jiayi Wang & @markrobinsonca.bsky.social in the multi-sample/-condition/-subpopulation theme: ...
Disentangling cell type and state transcriptional programs https://www.biorxiv.org/content/10.1101/2024.11.29.626057v1
Disentangling cell type and state transcriptional programs https://www.biorxiv.org/content/10.1101/2024.11.29.626057v1
Single-cell omics approaches profile molecular constituents of individual cells. Replicated multi-co
www.biorxiv.org
December 4, 2024 at 11:47 AM
A little piece that's been in the works with former MSc, now PhD student, Jiayi Wang & @markrobinsonca.bsky.social in the multi-sample/-condition/-subpopulation theme: ...
Reposted by Methylrot
Academic job ads when there is an internal candidate.
November 30, 2024 at 12:14 PM
Academic job ads when there is an internal candidate.
Reposted by Methylrot
Here’s a visualization of all the curse words in real time, which is oddly satisfying:
swearsky.bagpuss.org
swearsky.bagpuss.org
SwearSky
Bluesky profanity, as it happens
swearsky.bagpuss.org
November 21, 2024 at 10:59 PM
Here’s a visualization of all the curse words in real time, which is oddly satisfying:
swearsky.bagpuss.org
swearsky.bagpuss.org
Reposted by Methylrot
New method for identifying spatially variable genes in spatial transcriptomics.
We use spectral graph theory to extract 1D curves related to tissue morphology, creating a more relevant coordinate system. Improves sensitivity.
with @PhillipNicol et al.
www.biorxiv.org/content/10.1...
We use spectral graph theory to extract 1D curves related to tissue morphology, creating a more relevant coordinate system. Improves sensitivity.
with @PhillipNicol et al.
www.biorxiv.org/content/10.1...
November 22, 2024 at 8:04 PM
New method for identifying spatially variable genes in spatial transcriptomics.
We use spectral graph theory to extract 1D curves related to tissue morphology, creating a more relevant coordinate system. Improves sensitivity.
with @PhillipNicol et al.
www.biorxiv.org/content/10.1...
We use spectral graph theory to extract 1D curves related to tissue morphology, creating a more relevant coordinate system. Improves sensitivity.
with @PhillipNicol et al.
www.biorxiv.org/content/10.1...
Reposted by Methylrot
I have a YouTube playlist (10 videos) for #MolecularBiology for my undergrad interns in the lab.
www.youtube.com/playlist?lis...
I usually have my interns watch these videos to get introduced to the basic concepts before I go show them how to in the lab.
www.youtube.com/playlist?lis...
I usually have my interns watch these videos to get introduced to the basic concepts before I go show them how to in the lab.
November 17, 2024 at 2:07 PM
I have a YouTube playlist (10 videos) for #MolecularBiology for my undergrad interns in the lab.
www.youtube.com/playlist?lis...
I usually have my interns watch these videos to get introduced to the basic concepts before I go show them how to in the lab.
www.youtube.com/playlist?lis...
I usually have my interns watch these videos to get introduced to the basic concepts before I go show them how to in the lab.
Reposted by Methylrot
Bluesky for Science
Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice
blog.stephenturner.us/p/bluesky-fo... 🧬🖥️🧪
Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice
blog.stephenturner.us/p/bluesky-fo... 🧬🖥️🧪
Bluesky for Science
Bluesky starter packs for genomics, bioinformatics, R, and Nextflow
blog.stephenturner.us
November 16, 2024 at 10:25 AM
Bluesky for Science
Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice
blog.stephenturner.us/p/bluesky-fo... 🧬🖥️🧪
Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice
blog.stephenturner.us/p/bluesky-fo... 🧬🖥️🧪
Reposted by Methylrot
We just released 8 new data wrangling tutorials for biologists! sandbox.bio/community/da... 💻 🧬
Data and Text Processing
Command-line tutorials on data and text processing, by Francisco M. Couto.
sandbox.bio
November 15, 2024 at 5:28 PM
We just released 8 new data wrangling tutorials for biologists! sandbox.bio/community/da... 💻 🧬
Reposted by Methylrot
I made a bot that posts pre-prints of single cell papers:
@prepub-singlecell.bsky.social
(I posted about it a little while ago when no one was here, so posting again now :D)
It's pretty dumb so very open to suggestions for improvements!
@prepub-singlecell.bsky.social
(I posted about it a little while ago when no one was here, so posting again now :D)
It's pretty dumb so very open to suggestions for improvements!
November 14, 2024 at 6:52 AM
I made a bot that posts pre-prints of single cell papers:
@prepub-singlecell.bsky.social
(I posted about it a little while ago when no one was here, so posting again now :D)
It's pretty dumb so very open to suggestions for improvements!
@prepub-singlecell.bsky.social
(I posted about it a little while ago when no one was here, so posting again now :D)
It's pretty dumb so very open to suggestions for improvements!
Reposted by Methylrot
Reminder for newcomers that bioRxiv has Bluesky accounts in every subject category - great way to keep up (please re-skeet) connect.biorxiv.org/news/2023/09...
bioRxiv expands on Mastodon and Bluesky
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
connect.biorxiv.org
November 10, 2024 at 1:40 PM
Reminder for newcomers that bioRxiv has Bluesky accounts in every subject category - great way to keep up (please re-skeet) connect.biorxiv.org/news/2023/09...