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Pixelator 0.18 series is here

· 2 min read

We are delighted to inform all our Pixelators that we are releasing new versions of our data processing pipeline (nf-core/pixelator, 1.3.0) and our pixelator software (0.18 series). These updates will support your experiments with our new Single Cell Spatial Proteomics Kit, Immunology Panel 2, Human v2 (product number PXGIMM002), or MPX v2.

The new version of Pixelator has improved sensitive algorithms to detect meaningful colocalizations and polarity. We also equipped pixelator to support layout calculations transforming your cellular graphs into 3D structures.

Changes in the sample sheet​

For successful processing data from MPX v2, we have a new panel called human-sc-immunology-spatial-proteomics-2 that you can use in your samplesheet of * nf-core/pixelator*. The old panel still works under human-sc-immunology-spatial-proteomics-1 for your old MPX v1 kits.

DSB​

We learnt about dsb, a method to denoise and normalize antibody-based assays on droplet-based platforms, that we have adapted to the characteristics of MPX. Pixelator can pool and normalize a series of experiments with dsb and we demonstrate it in our abundance normalization tutorials in Python and R.

Best 3D cell structures​

We have adapted recognized graph drawing techniques to MPX to obtain and visualize the best 3D cell structure possible in your data. We have decided on some default parameters that make this process seamless for our users and lay the data in the PXL file data structure before starting your MPX analysis workflow. The nitty gritty details are explained in greater detail in our algorithms section.

QC report​

We have updated many fields in the QC report that Pixelator outputs every time you process your data to make it more accurate to the new chemistry and after gathering feedback from our customers.

Software site​

Finally, we have vastly upgraded our software site with new technical information, artwork to explain difficult concepts, and new tutorials to guide your MPX v2 analysis to the next level.

We have released many other improvements and you can always access and read the more technically detailed release notes for pixelator, for pixelatorR and nf-core/pixelator.