Glossary
Component
A component is a subset of a graph where all nodes are connected, and no node in the subset is connected to any node outside it. pixelator produces components from MPX/PNA data that correspond to the spatial networks produced on the surface of cells. Graph components are qualified as cells after pixelator has carried out cell calling.
DNA pixels
DNA pixels and their use to map proteins in cell surfaces are a core innovation of Pixelgen Technologies. These are concatemer of DNA with predefined parts that allow MPX to be performed. For a brief introduction to MPX, check this document.
Edge
An edge is a connection between two nodes in a graph. It represents a relationship or link between the nodes, forming part of the graph's structure. In MPX/PNA data, an edge represents a spatial adjacency that is detected between two DNA pixels (MPX) or protein molecules (PNA).
Graph Layout
A graph layout is a way of arranging the nodes and edges of a graph in a visual space. The goal is typically to create a visually informative representation of the graph, minimizing clutter, overlapping elements, or ambiguity in the relationships between nodes.
In MPX and PNA data, graph layouts are used to create 3D representations of individual cells, which can be used to visually inspect the shape of the cell component, or spatial effects that are apparent in spatial statistics. There are many layout strategies and in our visualization tutorial we explore some of those.
MPX
Molecular Pixelation (MPX) is the name of the first generation of spatial network technology powering Pixelgen Technologies' assays.
Nextflow
Nextflow is a workflow orchestration engine with a domain specific language (DSL) syntax that enables scalable and reproducible scientific workflows using software containers. It is compatible with the most common scripting languages and configurable to deploy complex parallel and reactive workflows on clouds and clusters.
nf-core
A community effort to collect a curated set of analysis pipelines using Nextflow with an open source philosophy. Nf-core pipelines adhere to strict guidelines with versioning, allowing easy reproducibility and validated releases, perfect for academic facilities. Workflow developers can use companion templates and tools help to validate pipeline code and simplify common tasks.
nf-core/pixelator
nf-core/pixelator is the name of Pixelgen Technologies' nf-core open source workflow that is highly reliable, validated in different platforms and developed with reproducibility in mind.
Node
A node is a fundamental element in a graph, representing an entity or point. Nodes are connected to each other by edges, defining the graph's framework. In MPX/PNA data, each node represents a spatial location that has been sampled on the surface of a cell.
pixelator
Our software pixelator is the library with the underlying logic for processing and analyzing MPX and PNA data, from raw FASTQ reads to PXL files. Pixelgen Technologies packages this library in software containers in order to use it as companion of nf-core/pixelator, creating highly reproducible workflows.
pixelatorR
pixelatorR is the R version of the pixelator library that can be used to analyze MPX and PNA data.
PNA
Proximity Network Assay (PNA) is the name of the second generation of spatial network technology powering Pixelgen Technologies' assays.
UMI
UMIs (Unique Molecular Identifiers) are tags made of unique nucleotide combinations attached to a molecule in order to provide with means to uniquely identify that particular molecule before amplification (e.g. PCR) and thus reduce quantitation biases Kivioja et al., 2011. MPX and PNA use UMIs in order to uniquely count antibody molecules.
UPI
The UPI is a randomly generated nucleotide sequence, and each MPX DNA pixel concatemer includes multiple repeated copies of it. Following the MPX assay, each read contains a UPIA and a UPIB sequence, corresponding to the two rounds of pixelation. These sequences enable the mapping of the UMI to its originating pixel A and pixel B.