one codex database (Akoya Biosciences)

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Akoya Biosciences one codex database
One Codex Database, supplied by Akoya Biosciences, used in various techniques. Bioz Stars score: 99/100, based on 12616 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/fusion+data+analysis+software+program/PhenoCycler-Fusion+2%2E0/pmc10065446-393-20-21
Average 99 stars, based on 12616 article reviews

one codex database - by Bioz Stars, 2026-09

99/100 stars

Images

Inverted Microscopy:

Article Title: Longitudinal spatial neutrophil profiling during ACT in murine melanoma reveals distinct lymph node infiltration patterns.
Article Snippet: All antibodies were conjugated in-house to oligonucleotide sequences synthesized by biomers.net GmbH. .. Images were acquired on a PhenoCycler-Fusion (Akoya Biosciences) coupled to a Zeiss Axio Observer 7 inverted microscope through the CODEX Instrument Manager (CIM; Akoya Biosciences) and ZEN (Zeiss) softwares. ..

Formalin-fixed Paraffin-Embedded:

Article Title: Cellular architecture and neighborhood-informed virtual spatial tumor profiling from histopathology.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Formalin-fixed paraffin-embedded (FFPE) human lung tumor samples This Manuscript N/A Chemicals, peptides, and recombinant proteins CODEX barcode BX-023 (used for CD163 custom conjugation) Akoya Biosciences Cat# 5250003 CODEX barcode BX-052 (used for FAP custom conjugation) Akoya Biosciences Cat# 5250012 CODEX barcode BX-016 (used for CD138 custom conjugation) Akoya Biosciences Cat# 5150001 CODEX barcode BX-020 (used for CD66b custom conjugation) Akoya Biosciences Cat# 5250002 CODEX barcode BX-013 (used for αSMA custom conjugation) Akoya Biosciences Cat# 5450017 CODEX barcode BX-028 (used for MMP9 custom conjugation) Akoya Biosciences Cat# 5150005 Deposited data CODEX and H&E data This paper Zenodo: https://zenodo.org/records/ 20263843 Software and algorithms R 4.4.0 R Core Team https://www.r-project.org Python 3.10.14 Python Software Foundation https://www.python.org/downloads/ release/python-31014/ CODEX Instrument Manager Akoya Biosciences https://help.codex.bio/codex/cim/ CODEX Processor Akoya Biosciences https://help.codex.bio/codex/processor/ ImageJ v2.3.0 ImageJ https://imagej.net/ij/ QuPath v0.4.3 QuPath https://qupath.github.io/ Seurat 5.1.0 Satija Lab https://satijalab.org/seurat Harmony 1.2.1 CRAN https://cran.r-project.org/web/packages/ harmony/index.html mclust 6.1.1 CRAN https://cran.r-project.org/package=mclust ConsensusClusterPlus 1.68.0 Bioconductor https://bioconductor.org/packages/ release/bioc/html/ConsensusClusterPlus. html GSVA 1.52.3 Bioconductor https://www.bioconductor.org/packages/ release/bioc/html/GSVA.html survival 3.6-4 CRAN https://cran.r-project.org/ package=survival survminer 0.5.0 CRAN https://cran.r-project.org/ package=survminer randomForestSRC 3.3.2 CRAN https://cran.r-project.org/ package=randomForestSRC CANVAS pipeline and analysis scripts This paper GitHub: https://github.com/lilab-stanford/ CANVAS Other PhenoCycler Antibody Conjugation Kit Akoya Biosciences Cat# 7000009 PhenoCycler Assay Reagent Akoya Biosciences Cat# 7000002 10X Buffer Kit for PhenoCycler-Fusion Akoya Biosciences Cat# 7000019 CODEX Storage Buffer Akoya Biosciences Cat# 232107 ll OPEN ACCESS Cell 189, 1–19.e1–e9, July 9, 2026 e2 Article ..

Recombinant:

Conjugation Assay:

Software:

Article Title: Lymph node microenvironment remodeling unlocks local antibody-mediated B cell depletion.
Article Snippet: Image acquisition was carried out using the Keyence BZ- X810 fluorescence microscope equipped with a 20× air objective. .. Following PhenoCycler acquisition, images were processed using the PhenoCycler Processor software (Akoya Biosciences). .. Cell segmentation was performed using the MACSiQ software (Miltenyi), followed by cell phenotyping using the open- source spatial analysis platform CytoMAP (Stoltzfus et al., 2020) and the MACSiQ suite.

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