#NatMethods
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haoyin.bsky.social
Optical clearing & time-lapse fluorescent imaging of Live mouse Brain (up to 800 μm of depth)🤯

An acute olfactory bulb slice(P11) loaded with GCaMP6f (Ca2+ sensor) was imaged with #2PM at a depth of 150 μm during clearing with SeeDB-Live👹

#NatMethods 2026
www.nature.com/articles/s41...
March 14, 2026 at 12:34 PM
haoyin.bsky.social
#SpatialOmics

MCMICRO
Multiple Choice Microscopy pipeline
mcmicro.org

Multi-channel whole-slide images▶️
Single-cell data + Spatial Feature Tables

Multimodal (CyCIF CODEX mIHC) registration + HE IMC MIBI

#NatMethods 2022
www.nature.com/articles/s41...
October 12, 2025 at 12:21 PM
haoyin.bsky.social
Subcellular resolution (333 nm) Imaging Mass Cytometry🤠

Oversampling + point spread function image deconvolution

Executable on Hyperion XTi or Hyperion+ system

Resolving Nucleoli, neighboring B-T cells

25 plex Ab

#NatMethods 2025
www.nature.com/articles/s41...
November 1, 2025 at 10:54 AM
haoyin.bsky.social
Spatial mechano-transcriptomics👹

Image-based cell mechanics inference
Segmentation Multi-junctional molecules▶️
Circular arc polygon tiling for cell contacts▶️
Cellular pressure, junctional tension, stress tensor

+Imaging-based #SpatialTranscriptomics

#NatMethods 2025
www.nature.com/articles/s41...
April 9, 2025 at 12:02 PM
haoyin.bsky.social
#SpatialTranscriptomics

Optimizing Xenium In Situ data utility by quality assessment & best-practice analysis workflows

Must-read for Xenium user🔥

👉Segmentation
👉Spatially variable feature selection
👉Imputation
👉Spatial domain identification

#NatMethods 2025
www.nature.com/articles/s41...
March 7, 2026 at 1:41 PM
haoyin.bsky.social
Spatial Multi-omics

DBiTplus
DBiT-seq + CODEX

Mesmer segmentation
MaxFus multiomic integration
CODEX-informed spatial deconvolution (TACCO vs Cell2location vs RCTD)

Work on FFPE
>1000 genes/25 μm spot

@zongmingma.bsky.social @rongfan8.bsky.social #NatMethods 2025
www.nature.com/articles/s41...
January 16, 2026 at 8:08 PM
haoyin.bsky.social
SpatioTemporal Omics eneRgIES

STORIES
Learning Waddington differentiation potential (FGW loss) from #SpatialTranscriptomics (across time points) using Optimal Transport

Tunable weights of spatial information

Compute both pseudotime & velocity

#NatMethods 2025
www.nature.com/articles/s41...
March 10, 2026 at 12:08 PM
realbiomassspec.bsky.social
Empowering chemists to mine high-throughput mass spectrometry datasets #NatMethods www.nature.com/articles/s41...
Empowering chemists to mine high-throughput mass spectrometry datasets - Nature Methods
The Mass Query Language (MassQL) enables scientists to precisely express and reproducibly search for mass spectrometry (MS) peak patterns in large MS datasets. MassQL has been adopted across the most ...
www.nature.com
May 14, 2025 at 5:47 PM
haoyin.bsky.social
Neural organoid response (Cell type speciation, axial patterning) to morphogens
A systematic scRNA-seq screening

Round1️⃣
👉8 morphogens (CHIR XAV939 SHH Cyclopamine FGF8b RA BMP4/7)
👉3 hPSC lines
👉97 conditions

Round2️⃣
👉Morphogen combos
👉12 conditions

#NatMethods 2025
www.nature.com/articles/s41...
April 8, 2026 at 10:42 AM
realbiomassspec.bsky.social
Uncovering hidden protein modifications with native top-down mass spectrometry #NatMethods www.nature.com/articles/s41...
Uncovering hidden protein modifications with native top-down mass spectrometry - Nature Methods
precisION discovers, localizes and quantifies protein modifications within complex proteoform assemblies through data-driven analysis of native top-down mass spectra.
www.nature.com
September 30, 2025 at 6:10 PM
brainbyana.bsky.social
🚨 New in Nat Methods: "Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing"

DOI: doi.org/10.1038/s415...

#Genomics #NatMethods #Transcriptomics #SDRseq #Science #SingleCell
Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing - Nature Methods
This study introduces SDR-seq, a droplet-based single-cell DNA–RNA sequencing platform, enabling the study of gene expression profiles linked to both noncoding and coding variants.
doi.org
September 9, 2025 at 9:04 AM
realbiomassspec.bsky.social
Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry #NatMethods www.nature.com/articles/s41...
Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry - Nature Methods
An ion mobility-resolved mass cytometry method for single-cell metabolomics enables multidimensional metabolomic profiling. The approach was used to curate a metabolic single-cell atlas containing 45,...
www.nature.com
February 13, 2026 at 8:32 PM
realbiomassspec.bsky.social
MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries #NatMethods www.nature.com/articles/s41...
MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries - Nature Methods
MSnLib is a large-scale, open MSn spectral library featuring >2.3 million MSn and >357,000 MS2 spectra for 30,008 unique small molecules.
www.nature.com
September 16, 2025 at 3:05 PM
realbiomassspec.bsky.social
Unified mass imaging maps the lipidome of vertebrate development #NatMethods #MassSpec www.nature.com/articles/s41...
Unified mass imaging maps the lipidome of vertebrate development - Nature Methods
uMAIA is an analytical framework designed to enable the construction of metabolic atlases at high resolution using mass spectrometry imaging data.
www.nature.com
September 4, 2025 at 12:03 PM
realbiomassspec.bsky.social
A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data #NatMethods www.nature.com/articles/s41...
A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods
Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...
www.nature.com
July 2, 2025 at 1:25 PM
realbiomassspec.bsky.social
A universal language for finding mass spectrometry data patterns #NatMethods www.nature.com/articles/s41...
A universal language for finding mass spectrometry data patterns - Nature Methods
The Mass Spectrometry Query Language (MassQL) is an open-source language that enables instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and ex...
www.nature.com
May 14, 2025 at 5:47 PM