#CellSegmentation
Benchmarking segmentation methods for Spatial Transcriptomics
11 methods
5 ST modalities
Watershed, BIDCell, Cellpose, SCS, SAM, SAM2, mSAM, Baysor, CelloType, Swin-s, Mask R-CNN
Stereo-seq, Xenium, CosMx, STARmap PLUS, MERFISH
#NatMethods 2026
www.nature.com/articles/s41...
Benchmarking segmentation methods for Spatial Transcriptomics
11 methods
5 ST modalities
Watershed, BIDCell, Cellpose, SCS, SAM, SAM2, mSAM, Baysor, CelloType, Swin-s, Mask R-CNN
Stereo-seq, Xenium, CosMx, STARmap PLUS, MERFISH
#NatMethods 2026
www.nature.com/articles/s41...
October 31, 2026 at 12:07 PM
#CellSegmentation
Benchmarking segmentation methods for Spatial Transcriptomics
11 methods
5 ST modalities
Watershed, BIDCell, Cellpose, SCS, SAM, SAM2, mSAM, Baysor, CelloType, Swin-s, Mask R-CNN
Stereo-seq, Xenium, CosMx, STARmap PLUS, MERFISH
#NatMethods 2026
www.nature.com/articles/s41...
Benchmarking segmentation methods for Spatial Transcriptomics
11 methods
5 ST modalities
Watershed, BIDCell, Cellpose, SCS, SAM, SAM2, mSAM, Baysor, CelloType, Swin-s, Mask R-CNN
Stereo-seq, Xenium, CosMx, STARmap PLUS, MERFISH
#NatMethods 2026
www.nature.com/articles/s41...
🧪 How can researchers turn spatial biology into translational discoveries? Hear from UMass Chan & Alnylam on building MERFISH workflows and analysis infrastructure. Can’t attend live? Register for on-demand access.
📅 Nov 4 | 8 AM PT / 11 AM ET
www.labroots.com/ms/webinar/b...
📅 Nov 4 | 8 AM PT / 11 AM ET
www.labroots.com/ms/webinar/b...
November 3, 2026 at 5:07 PM
🧪 How can researchers turn spatial biology into translational discoveries? Hear from UMass Chan & Alnylam on building MERFISH workflows and analysis infrastructure. Can’t attend live? Register for on-demand access.
📅 Nov 4 | 8 AM PT / 11 AM ET
www.labroots.com/ms/webinar/b...
📅 Nov 4 | 8 AM PT / 11 AM ET
www.labroots.com/ms/webinar/b...
Segmentation references likely differ across Stereo-seq, Xenium, CosMx, STARmap PLUS and MERFISH. Reporting downstream effects too, such as cell-type calls and marker purity, would help, since boundary overlap alone can rank methods differently.
November 1, 2026 at 8:06 PM
Segmentation references likely differ across Stereo-seq, Xenium, CosMx, STARmap PLUS and MERFISH. Reporting downstream effects too, such as cell-type calls and marker purity, would help, since boundary overlap alone can rank methods differently.
🧪 How can researchers turn spatial biology into translational discoveries? Hear from UMass Chan & Alnylam on building MERFISH workflows and analysis infrastructure. Can’t attend live? Register for on-demand access.
📅 Nov 4 | 8 AM PT / 11 AM ET
buff.ly/9itrWBY
📅 Nov 4 | 8 AM PT / 11 AM ET
buff.ly/9itrWBY
October 22, 2026 at 4:06 PM
🧪 How can researchers turn spatial biology into translational discoveries? Hear from UMass Chan & Alnylam on building MERFISH workflows and analysis infrastructure. Can’t attend live? Register for on-demand access.
📅 Nov 4 | 8 AM PT / 11 AM ET
buff.ly/9itrWBY
📅 Nov 4 | 8 AM PT / 11 AM ET
buff.ly/9itrWBY
the tables provide no estimate of the false positive and negative rates for the merfish data, which are not negligible
October 22, 2026 at 2:22 PM
the tables provide no estimate of the false positive and negative rates for the merfish data, which are not negligible
Benchmarking segmentation methods for spatial transcriptomics
->Nature | More on "Spatial transcriptomics segmentation methods" at BigEarthData.ai
->Nature | More on "Spatial transcriptomics segmentation methods" at BigEarthData.ai
Benchmarking segmentation methods for spatial transcriptomics
We evaluated 11 segmentation methods (Watershed, BIDCell, Cellpose, SCS, SAM, SAM2, mSAM, Baysor, CelloType, Swin-s and Mask R-CNN) across 15 spatial transcriptomics datasets generated using 5 different technologies: Stereo-seq, Xenium, CosMx, STARmap PLUS and MERFISH (Fig. 1a, Supplementary Table 1 and Methods). The datasets span two species (mouse and human), 12 tissue types (brain, breast, embryo, lung, pancreas, skin, colon, stomach, ovarian, kidney, prostate and utero) and a wide range of cell counts, from around 700 cells in an ovarian cancer dataset to large cohorts of more than 800,000 cells in a prostate cancer dataset. We selected this diversity to reflect the breadth of contemporary spatial transcriptomics applications and to challenge segmentation robustness under heterogeneous biological and technical conditions (Supplementary Fig. 1a,b). We also performed cross-technology benchmarking (Fig. 1b) to account for discrepancies between platforms. This design separated algorithm-specific effects from platform-dependent biases. We conducted all the analysis using a unified benchmarking pipeline (Fig. 1c) that applies standardized quality control (QC), patch-based processing and consistent preprocessing across methods to ensure fair and reproducible comparisons. During preprocessing, we established data subsetting criteria for each dataset and method based on technical limitations (Methods). For methods that explicitly integrate transcriptomic information into their...
www.nature.com
October 23, 2026 at 7:58 PM
3/ Then came spatial. 10x Visium, Slide-seq, MERFISH. Each with different data structures, quirks, and analysis hurdles. Overwhelming? Yes.
October 12, 2026 at 1:45 PM
3/ Then came spatial. 10x Visium, Slide-seq, MERFISH. Each with different data structures, quirks, and analysis hurdles. Overwhelming? Yes.
3D MERFISH reveals cell-type diversity generated by mRNA partitioning in spiralian embryogenesis https://www.biorxiv.org/content/10.64898/2026.10.05.756875v1
October 7, 2026 at 8:16 AM
3D MERFISH reveals cell-type diversity generated by mRNA partitioning in spiralian embryogenesis https://www.biorxiv.org/content/10.64898/2026.10.05.756875v1
3D MERFISH reveals cell-type diversity generated by mRNA partitioning in spiralian embryogenesis https://www.biorxiv.org/content/10.64898/2026.10.05.756875v1
October 7, 2026 at 8:16 AM
3D MERFISH reveals cell-type diversity generated by mRNA partitioning in spiralian embryogenesis https://www.biorxiv.org/content/10.64898/2026.10.05.756875v1
MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue https://www.biorxiv.org/content/10.64898/2026.10.06.756924v1
October 6, 2026 at 4:48 PM
MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue https://www.biorxiv.org/content/10.64898/2026.10.06.756924v1
MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue https://www.biorxiv.org/content/10.64898/2026.10.06.756924v1
October 6, 2026 at 4:48 PM
MERFISH-based pooled genetic screening reveals cell non-autonomous phenotypes in intact tissue https://www.biorxiv.org/content/10.64898/2026.10.06.756924v1
😮
Whole- #transcriptome -scale isoform-resolved spatial imaging of single #cells in tissues: Cell www.cell.com/cell/fulltex...
Whole- #transcriptome -scale isoform-resolved spatial imaging of single #cells in tissues: Cell www.cell.com/cell/fulltex...
Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues
RT&T-AMP-MERFISH enables whole-transcriptome-scale, isoform-resolved spatial imaging
of single cells in intact tissues and reveals how gene programs and transcript isoform
usage vary across cell types...
www.cell.com
September 28, 2026 at 9:41 PM
😮
Whole- #transcriptome -scale isoform-resolved spatial imaging of single #cells in tissues: Cell www.cell.com/cell/fulltex...
Whole- #transcriptome -scale isoform-resolved spatial imaging of single #cells in tissues: Cell www.cell.com/cell/fulltex...
Mapped the olfactory system in mice using MERFISH, revealing distinct expression patterns of 100+ olfactory receptors vital for social odor detection and processing. PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
No description available
www.cell.com
September 21, 2026 at 4:00 AM
whole-transcriptome merfish
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues
RT&T-AMP-MERFISH enables whole-transcriptome-scale, isoform-resolved spatial imaging
of single cells in intact tissues and reveals how gene programs and transcript isoform
usage vary across cell types...
www.cell.com
September 17, 2026 at 6:47 PM
whole-transcriptome merfish
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Except the MerFish of course.
You can hardly expect the cod and halibut to actually stand. Those fuckers are way too slippery. So they can flop in tank things or close to the beach.
But MerFish. Naturals. Up on their little flippers. Sliding to & fro, bresticles clothed in subtle hair, shimmering,
You can hardly expect the cod and halibut to actually stand. Those fuckers are way too slippery. So they can flop in tank things or close to the beach.
But MerFish. Naturals. Up on their little flippers. Sliding to & fro, bresticles clothed in subtle hair, shimmering,
September 14, 2026 at 9:28 PM
Except the MerFish of course.
You can hardly expect the cod and halibut to actually stand. Those fuckers are way too slippery. So they can flop in tank things or close to the beach.
But MerFish. Naturals. Up on their little flippers. Sliding to & fro, bresticles clothed in subtle hair, shimmering,
You can hardly expect the cod and halibut to actually stand. Those fuckers are way too slippery. So they can flop in tank things or close to the beach.
But MerFish. Naturals. Up on their little flippers. Sliding to & fro, bresticles clothed in subtle hair, shimmering,
New study reveals mapping of olfactory receptors in MoE & OB using MERFISH, showing how social odors influence mouse behavior. Key insights on 100+ ORs! PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
No description available
www.cell.com
September 15, 2026 at 12:00 AM
September 14, 2026 at 3:50 AM
New research reveals the spatial organization of olfactory receptors in mice, highlighting 100+ distinct ORs mapped in the MOE & OB via MERFISH, crucial for social odor detection. PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2 #Medsky #Pharmsky #RNA #ASHG 🧪
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
No description available
www.cell.com
September 9, 2026 at 9:00 PM
Using real imaging-based spatial transcriptomics (MERFISH) data of bacteria, STARIT identifies cells with similar overall exp magnitude but distinct subcellular organization: showing more punctuated vs diffuse transcript localization for flagellar subunits, with potential functional consequences.
September 9, 2026 at 1:32 PM
Using real imaging-based spatial transcriptomics (MERFISH) data of bacteria, STARIT identifies cells with similar overall exp magnitude but distinct subcellular organization: showing more punctuated vs diffuse transcript localization for flagellar subunits, with potential functional consequences.
A comprehensive MERFISH analysis reveals the spatial mapping of olfactory receptor expression in the MOE and OB, crucial for detecting social odors in mice. PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
No description available
www.cell.com
September 5, 2026 at 10:00 PM
A shout-out as well to Jonathan Enriquez (Institut de Génomique Fonctionnelle de Lyon) & @yinanwan.bsky.social (University of Basel) for the MERFISH talks, followed by a hands-on session led by Dorottya Ralbovszki (BRIC University of Copenhagen) & @tarcsavirg.bsky.social (ELTE).🔬🧵
September 4, 2026 at 7:40 PM
A shout-out as well to Jonathan Enriquez (Institut de Génomique Fonctionnelle de Lyon) & @yinanwan.bsky.social (University of Basel) for the MERFISH talks, followed by a hands-on session led by Dorottya Ralbovszki (BRIC University of Copenhagen) & @tarcsavirg.bsky.social (ELTE).🔬🧵
A novel MERFISH approach reveals a detailed molecular atlas of olfactory receptor expression in the MOE and OB, shedding light on how mice detect social odors. Key findings include systematic mapping crucial… PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
No description available
www.cell.com
September 1, 2026 at 5:00 PM
A novel MERFISH approach reveals a detailed molecular atlas of olfactory receptor expression in the MOE and OB, shedding light on how mice detect social odors. Key findings include systematic mapping crucial… PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
Revolutionary MERFISH reveals the mapping of olfactory receptor expression in MOE & OB. Key findings detail spatial organization for social odors, impacting mouse behavior. Fascinating insights into sensory… PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
No description available
www.cell.com
August 31, 2026 at 12:00 AM
Revolutionary MERFISH reveals the mapping of olfactory receptor expression in MOE & OB. Key findings detail spatial organization for social odors, impacting mouse behavior. Fascinating insights into sensory… PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
New study maps olfactory receptor expression in mice using MERFISH, revealing how social odors are detected in the main olfactory epithelium (MOE) and bulb (OB). Key findings highlight the organized sensory… PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
No description available
www.cell.com
August 28, 2026 at 6:00 AM
New study maps olfactory receptor expression in mice using MERFISH, revealing how social odors are detected in the main olfactory epithelium (MOE) and bulb (OB). Key findings highlight the organized sensory… PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
A MERFISH study reveals the intricate mapping of 100+ olfactory receptors in the mouse primary olfactory system, crucial for detecting social odors and more. PMID:42054995, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
https://www.cell.com/cell/fulltext/S0092-8674(26)00389-2
No description available
www.cell.com
August 21, 2026 at 4:00 AM