🚨 New paper published in @natmethods.nature.com!
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods
SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...
nature.com
June 6, 2025 at 12:03 PM
🚨 New paper published in @natmethods.nature.com!
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
SpotSweeper: spatially aware quality control for spatial transcriptomics👍
www.nature.com/articles/s41...
www.nature.com/articles/s41...
SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods
SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...
www.nature.com
June 7, 2025 at 5:26 AM
SpotSweeper: spatially aware quality control for spatial transcriptomics👍
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Quality control matters in spatial transcriptomics. Check out this paper from Guo and colleagues on SpotSweeper that corrects for both local and regional artifacts across diverse technologies. www.nature.com/articles/s41...
SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods
SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...
www.nature.com
June 6, 2025 at 5:35 PM
Quality control matters in spatial transcriptomics. Check out this paper from Guo and colleagues on SpotSweeper that corrects for both local and regional artifacts across diverse technologies. www.nature.com/articles/s41...
#SpotSweeper is now published!
Check our journal club session summary of the pre-print version by @lahuuki.bsky.social
The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data!
youtu.be/f72XcXmtkfw?...
Check our journal club session summary of the pre-print version by @lahuuki.bsky.social
The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data!
youtu.be/f72XcXmtkfw?...
June 10, 2025 at 2:48 PM
#SpotSweeper is now published!
Check our journal club session summary of the pre-print version by @lahuuki.bsky.social
The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data!
youtu.be/f72XcXmtkfw?...
Check our journal club session summary of the pre-print version by @lahuuki.bsky.social
The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data!
youtu.be/f72XcXmtkfw?...
Like the game minesweeper, SpotSweeper overcomes this limitation by using the information from nearest neighbors to flag problematic local outliers 😎
June 6, 2025 at 12:03 PM
Like the game minesweeper, SpotSweeper overcomes this limitation by using the information from nearest neighbors to flag problematic local outliers 😎
🤔Could quality control create more harm than good? We explore this question in the context of #SRT.
SpotSweeper is developed to combat implicit selection bias.
Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social
👉: bsky.app/profile/mict...
SpotSweeper is developed to combat implicit selection bias.
Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social
👉: bsky.app/profile/mict...
Quality control matters in spatial transcriptomics. Check out this paper from Guo and colleagues on SpotSweeper that corrects for both local and regional artifacts across diverse technologies. www.nature.com/articles/s41...
SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods
SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...
www.nature.com
June 6, 2025 at 7:08 PM
🤔Could quality control create more harm than good? We explore this question in the context of #SRT.
SpotSweeper is developed to combat implicit selection bias.
Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social
👉: bsky.app/profile/mict...
SpotSweeper is developed to combat implicit selection bias.
Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social
👉: bsky.app/profile/mict...
A big update from the preprint, we now show that SpotSweeper works across tissue types and sequencing-based technologies.
June 6, 2025 at 12:03 PM
A big update from the preprint, we now show that SpotSweeper works across tissue types and sequencing-based technologies.
Using this approach, we show that SpotSweeper successfully retains high quality observations while accurately detecting problematic local outliers in human DLPFC samples.
June 6, 2025 at 12:03 PM
Using this approach, we show that SpotSweeper successfully retains high quality observations while accurately detecting problematic local outliers in human DLPFC samples.
Weekly Reads 1/6/25
🔥 Taurine fuels leukemia stem cells via glycolysis
🧼 SpotSweeper: spatial QC gets smarter
🌐 scVIVA: niche-aware modeling of cell states in tissue
open.substack.com/pub/behindth...
#SingleCell #SpatialTranscriptomics #CancerBiology #Bioinformatics #SystemsBiology #AI
🔥 Taurine fuels leukemia stem cells via glycolysis
🧼 SpotSweeper: spatial QC gets smarter
🌐 scVIVA: niche-aware modeling of cell states in tissue
open.substack.com/pub/behindth...
#SingleCell #SpatialTranscriptomics #CancerBiology #Bioinformatics #SystemsBiology #AI
Weekly reads 1/6/25
From cancer ecosystems to cell state embeddings: context is everything
open.substack.com
June 8, 2025 at 10:24 AM
Weekly Reads 1/6/25
🔥 Taurine fuels leukemia stem cells via glycolysis
🧼 SpotSweeper: spatial QC gets smarter
🌐 scVIVA: niche-aware modeling of cell states in tissue
open.substack.com/pub/behindth...
#SingleCell #SpatialTranscriptomics #CancerBiology #Bioinformatics #SystemsBiology #AI
🔥 Taurine fuels leukemia stem cells via glycolysis
🧼 SpotSweeper: spatial QC gets smarter
🌐 scVIVA: niche-aware modeling of cell states in tissue
open.substack.com/pub/behindth...
#SingleCell #SpatialTranscriptomics #CancerBiology #Bioinformatics #SystemsBiology #AI
SpotSweeper also addresses a second big problem in spatial transcriptomics: the detection of regional artifacts that may arise due to sample prep.
June 6, 2025 at 12:03 PM
SpotSweeper also addresses a second big problem in spatial transcriptomics: the detection of regional artifacts that may arise due to sample prep.
SpotSweeper is able to accurately identify these artifacts using the multiscale local variance of mito %. Removal of these hangnails improves downstream results, such as marker gene detection.
June 6, 2025 at 12:03 PM
SpotSweeper is able to accurately identify these artifacts using the multiscale local variance of mito %. Removal of these hangnails improves downstream results, such as marker gene detection.
You don't want to miss out on this manuscript. For 𝑛𝑒𝑢𝑟𝑜𝑏𝑖𝑜𝑙𝑜𝑔𝑖𝑠𝑡𝑠, we have some very interesting findings 😉. For 𝑐𝑜𝑚𝑝𝑢𝑡𝑎𝑡𝑖𝑜𝑛𝑎𝑙 𝑚𝑒𝑡ℎ𝑜𝑑𝑜𝑙𝑜𝑔𝑖𝑠𝑡𝑠, the project has been a source of limitless creativity and innovation, including hashtag#SpotSweeper published in hashtag#NatureMethods.
February 20, 2026 at 8:18 PM
You don't want to miss out on this manuscript. For 𝑛𝑒𝑢𝑟𝑜𝑏𝑖𝑜𝑙𝑜𝑔𝑖𝑠𝑡𝑠, we have some very interesting findings 😉. For 𝑐𝑜𝑚𝑝𝑢𝑡𝑎𝑡𝑖𝑜𝑛𝑎𝑙 𝑚𝑒𝑡ℎ𝑜𝑑𝑜𝑙𝑜𝑔𝑖𝑠𝑡𝑠, the project has been a source of limitless creativity and innovation, including hashtag#SpotSweeper published in hashtag#NatureMethods.
We also include a lot of extended/supplementary data in this paper, such as parameter selection and the use of SpotSweeper on VisiumHD and imaging-based technologies. See the paper and discussion for more details on these issues!
June 6, 2025 at 12:03 PM
We also include a lot of extended/supplementary data in this paper, such as parameter selection and the use of SpotSweeper on VisiumHD and imaging-based technologies. See the paper and discussion for more details on these issues!
🚨 New blogpost alert!
I have written a blogpost on SpotSweeper, a bioconductor package to implement a SPATIALLY AWARE method for the quality control (QC) of spatial transcroptomic data.
Check it out! 🙏
#spatialbiology #omics #transcriptomics #QC 🧪
nonlinear-thoughts.netlify.app/posts/srt-qc...
I have written a blogpost on SpotSweeper, a bioconductor package to implement a SPATIALLY AWARE method for the quality control (QC) of spatial transcroptomic data.
Check it out! 🙏
#spatialbiology #omics #transcriptomics #QC 🧪
nonlinear-thoughts.netlify.app/posts/srt-qc...
Spatially aware quality control of spatial transcriptomic data using SpotSweeper – Tamim’s Blog
nonlinear-thoughts.netlify.app
January 7, 2026 at 1:29 PM
🚨 New blogpost alert!
I have written a blogpost on SpotSweeper, a bioconductor package to implement a SPATIALLY AWARE method for the quality control (QC) of spatial transcroptomic data.
Check it out! 🙏
#spatialbiology #omics #transcriptomics #QC 🧪
nonlinear-thoughts.netlify.app/posts/srt-qc...
I have written a blogpost on SpotSweeper, a bioconductor package to implement a SPATIALLY AWARE method for the quality control (QC) of spatial transcroptomic data.
Check it out! 🙏
#spatialbiology #omics #transcriptomics #QC 🧪
nonlinear-thoughts.netlify.app/posts/srt-qc...
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem https://www.biorxiv.org/content/10.64898/2025.12.06.692760v1
December 10, 2025 at 6:47 AM
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem https://www.biorxiv.org/content/10.64898/2025.12.06.692760v1
SpotSweeper: spatially-aware quality control for spatial transcriptomics https://www.biorxiv.org/content/10.1101/2024.06.06.597765v1
SpotSweeper: spatially-aware quality control for spatial transcriptomics https://www.biorxiv.org/content/10.1101/2024.06.06.597765v1
Quality control (QC) is a crucial step to ensure the reliability and accuracy of the data obtained f
www.biorxiv.org
June 9, 2024 at 6:46 PM
SpotSweeper: spatially-aware quality control for spatial transcriptomics https://www.biorxiv.org/content/10.1101/2024.06.06.597765v1
#BOG25 SH: Spots on image don't necessarily correspond to cells. Instead of looking globally for normalization, compare locally because some cells/spots will just have less RNA. Call Spotsweeper. If look at mito%, see more uniformity using spotsweeper
May 8, 2025 at 5:46 PM
#BOG25 SH: Spots on image don't necessarily correspond to cells. Instead of looking globally for normalization, compare locally because some cells/spots will just have less RNA. Call Spotsweeper. If look at mito%, see more uniformity using spotsweeper
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem https://www.biorxiv.org/content/10.64898/2025.12.06.692760v1
December 10, 2025 at 6:47 AM
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem https://www.biorxiv.org/content/10.64898/2025.12.06.692760v1
SpotSweeper: spatially-aware quality control for spatial transcriptomics https://www.biorxiv.org/content/10.1101/2024.06.06.597765v1
SpotSweeper: spatially-aware quality control for spatial transcriptomics https://www.biorxiv.org/content/10.1101/2024.06.06.597765v1
Quality control (QC) is a crucial step to ensure the reliability and accuracy of the data obtained f
www.biorxiv.org
June 9, 2024 at 6:46 PM
SpotSweeper: spatially-aware quality control for spatial transcriptomics https://www.biorxiv.org/content/10.1101/2024.06.06.597765v1
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem [new]
Spatial QC in Python: Locates artifacts, preserves tissue architecture.
Spatial QC in Python: Locates artifacts, preserves tissue architecture.
December 10, 2025 at 7:07 AM
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem [new]
Spatial QC in Python: Locates artifacts, preserves tissue architecture.
Spatial QC in Python: Locates artifacts, preserves tissue architecture.