CosMx® Analysis Scratch Space

Cellular neighborhoods: a useful, simple and flexible analysis framework

overview
An introduction to “cellular neighborhoods” and their many uses in analysis.
Oct 30, 2024
Patrick Danaher

Programmatic stitching with napari-cosmx

napari
how-tos
python
Did you know that napari-cosmx can stitch images from AtoMx™ SIP programmatically? In this post I show users who are comfortable with scripting how to stitch without directly using napari’s GUI.
Oct 18, 2024
Evelyn Metzger

New Features of AtoMx™ SIP v1.3.2

nanoU
NanoString University New Course Alert!
Oct 17, 2024
Evelyn Metzger

Stay up-to-date with our blog using your favorite RSS reader

rss
Don’t miss a post! This post shows you how to get automatic updates when there’s a new post.
Oct 17, 2024
Evelyn Metzger

Creating reference profiles for InSituType

cell typing
A short guide to creating reference profiles, and to merging profiles from different sources.
Aug 21, 2024
Patrick Danaher

How does background impact CosMx data, and when does it matter?

quality control
overview
CosMx data includes off-target “background” counts from off-target probe binding, appearing randomly at a low frequency across the dataset. In this article, we’ll discuss…
Aug 21, 2024
Patrick Danaher

InSituCor: an open-source package and AtoMx custom module for exploratory data analysis

AtoMx modules
exploratory analysis
We developed InSituCor as a tool for exploratory analysis of CosMx data; it has since become a mainstay of our in-house analyses. InSituCor reports on modules of “spatially…
Jul 18, 2024
Patrick Danaher

Using Squidpy with AtoMx™ SIP exports

Squidpy
python
visualization
AnnData
In this blog post, I’ll show how to prepare and analyze AtoMx™ SIP-exported CosMx® SMI data with python's squidpy package.
Jul 3, 2024
Evelyn Metzger

Comparing AtoMx™ SIP flat files with the legacy format

flat files
This short post shows differences between the AtoMx™ SIP-exported and legacy CosMx® SMI "flat files"
Jul 3, 2024
Evelyn Metzger

Applications for visualization and cell typing using ‘smoothed’ marker genes

visualization
cell typing
Applications for visualization and cell typing using ‘smoothed’ marker genes based on expression nearest neighbors
Jun 19, 2024
Dan McGuire

napari-cosmx essentials

napari
how-tos
visualization
python
In this post, I walk through some of the basic ways I use napari-cosmx to view and analyze SMI data. I will make use of this GUI/scripting duality and share a combination of GUI and programmatic tips and tricks.
Jun 17, 2024
Evelyn Metzger

Making composite images from layered morphology 2D images

Squidpy
Giotto
pre-processing
python
In this post, we describe a developmental python script that creates composite images from layered morphology 2D images.
Jun 12, 2024
Evelyn Metzger, Vikram Kohli

GeoMx® mask generation for marker-based single-cell application

GeoMx
how-tos
image processing
python
This post introduces a pipeline for automatic generating GeoMx® Digital Spatial Profiler (DSP)-ready binary masks in batch for marker-based single-cell application. Given the query marker protein of interest, the pipeline would take morphology images and generate binary masks for negative-stained cells and cells connecting to positive-stained regions, respectively. The pipeline runs as a command line and this post would serve as a guide to how it works and how to use it.
Jun 12, 2024
Lidan Wu

Creating an anndata object from AtoMx™ exported results for interactive viewer and python-based analysis

how-tos
visualization
Seurat
AnnData
python
This post describes how to create anndata object from AtoMx™ exported results. The resulting oject in ‘.h5ad’ format could be further analyzed using various python-based single-cell analysis tools, like scanpy and squidpy. Non-coders could also share the light-weighted data object, visualize and explore the processed data in several open-sourced interactive viewers, like Cirrocumulus and CELLxGENE viewers.
Jun 5, 2024
Lidan Wu

Vignette: Basics of CosMx Analysis in R

recommended
overview
quality control
normalization
cell typing
pre-processing
A complete demo analysis of a CosMx dataset can be found at workflow section in this post and the correspond scripts are stored under _code/vignette folder in this…
May 24, 2024
Patrick Danaher

FOV QC from single-cell gene expression in spatial dataset

quality control
pre-processing
This experimental approach is new as of April 2024 and is lightly tested. Please use thoughtfully while considering biological context.
May 20, 2024
Patrick Danaher

Evaluating Cell Segmentation Error based on Transcriptional Spatial Profiles using FastReseg

segmentation
algorithms
FastReseg algorithm scores individual transcripts for the goodness-of-fit within their respective cells based on the probability of each gene belonging to each cell type and the spatial dependency of transcript score. FastReseg can flag cells with putative cell segmentation errors and perform corrections rapidly.
May 15, 2024
Lidan Wu

Introduction to visualizing CosMx SMI data in Seurat

visualization
Seurat
Recommendations for spatial plots in Seurat
May 10, 2024
Claire Williams

Getting Started with the napari-cosmx plugin

visualization
napari
python
The AtoMx™ Spatial Informatics Portal (SIP) is an excellent solution for analyzing multi-omics spatial data generated on the CosMx® Spatial Molecular Imager (SMI). It offers…
May 1, 2024
Evelyn Metzger

 

The spatial algorithms zoo: recommended algorithms and efficient code

algorithms
Spatial statistics is a well-developed field, with deep statistical methodology and highly efficient open-source tools. In CosMx data, where a single study can contain…
Mar 20, 2024
Patrick Danaher

 

Cell typing: what we’ve found to work

cell typing
We cell type most studies using one of the following approaches:
Mar 12, 2024
Patrick Danaher

 

On the use of marker genes

cell typing
Our basic recommendation is this: relying on a few marker genes alone will not produce successful cell typing.
Mar 12, 2024
Patrick Danaher

 

Big datasets: strategies for memory-efficient analysis

big data
CosMx data can be truly huge, containing millions of cells and thousands of genes. This prevents many typical analysis strategies, including many toolkits designed for…
Mar 4, 2024
Patrick Danaher

QC and normalization of RNA data

quality control
normalization
pre-processing
We’ve tried a lot of options here, and we’ve settled on very simple procedures for most cases.
Jan 29, 2024
Patrick Danaher

Functions for condensing FOVs and tissues to minimize whitespace

visualization
Minimizing whitespace while plotting cells in xy space is a constant challenge. A single tissue will often have discontinuous FOVs, and aligning multiple tissues in a…
Jan 26, 2024
Patrick Danaher

Visualize cellular neighborhood in gallery mode

visualization
napari
A complete CosMx dataset will contain cell metadata, morphology/protein images and cell label results of cell segmentation. We’ve created a toolkit for visualizing the…
Jan 24, 2024
Lidan Wu, Patrick Danaher

The impact of segmentation error on differential expression analyses

segmentation
Cell segmentation is always imperfect, leaving some cells’ expression profiles contaminated with transcripts properly belonging to other cells. For many analyses, this is a…
Jan 24, 2024
Patrick Danaher

Inferring cell polygons from transcript locations

visualization
A complete CosMx dataset will contain polygonal boundaries for each cell for use in plotting. In practice, especially with earlier datasets or with datasets passed between…
Jan 5, 2024
Patrick Danaher

What is high-plex spatial transcriptomics for?

overview
High-plex single cell spatial transcriptomics data is a little awe-inspiring: even a perfunctory analysis of a single run produces a terabyte of data, gorgeous images, and…
Jan 5, 2024
Patrick Danaher
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