This repository provides access instructions and metadata for the imaging datasets associated with:

Wala & Christensen et al. 2026
Copanlisib in combination with nivolumab for microsatellite stable colorectal cancer: a phase 1/2 trial Nature Communications

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Overview

This dataset contains multiplexed immunofluorescence imaging data generated using:

• CyCIF (Cyclic Immunofluorescence)
• Orion (RareCyte Orion platform)

All images are provided in OME-TIFF format.

The data are hosted on Amazon S3 and can be accessed directly without authentication.

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Data location

All files are stored under the following S3 prefix:

s3://lsp-public-data/wala-christensen-2026-pik3ca-crc/

e.g. to list all files:

aws s3 ls s3://lsp-public-data/wala-christensen-2026-pik3ca-crc/ --recursive

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Directory structure

wala-christensen-2026-pik3ca-crc/
|
+-- cycif/
|   +-- LSP17708.ome.tif
|   +-- LSP17711.ome.tif
|   +-- ...
|
+-- orion/
    +-- LSP17707_...ome.tiff
    +-- LSP17710_...ome.tiff
    +-- ...

CyCIF directory

Contains Cyclic immunofluorescence images with the following channels:

Hoechst1	
A488	
A555	
A647	
Hoechst2	
CytochromeC	
pAKT	
LINE1	
Hoechst3	
pERK	
panCK	
pS6_240	
SMA	
Hoechst4	
Catenin	
CDX2	
gH2ax	
pS6_235	
Hoechst5	
PCNA	
MLH1	
HER2	
Ki67	
Hoechst6	
Vimentin	
H3K27me3	
TROP2	
CD44	
Hoechst7	
pNDRG1	
pRB	
p27

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Orion directory

Contains Orion multiplexed imaging data with the following channels:

Hoechst	
AF1	
CD31	
Ki67	
CD68	
CD163	
CD20	
CD4	
CD8a	
CD11c	
PDL1	
CD3e	
ECadherin	
PD1	
FOXP3	
CD45	
PanCK	
Blank	
SMA	

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Download instructions

Install AWS CLI: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html

Download entire dataset:

aws s3 sync \
  s3://lsp-public-data/wala-christensen-2026-pik3ca-crc/ \
  wala-christensen-2026-pik3ca-crc/ \
  --no-sign-request

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File format

All images are provided as:

OME-TIFF (.ome.tif / .ome.tiff)

Compatible software includes:

• napari
• FIJI / ImageJ (Bio-Formats)
• QuPath
• OMERO
• Python (ome-types, tifffile)

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Contact

For questions, please contact:

Jeremiah Wala, MD, PhD jeremiah_wala@dfci.harvard.edu