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Pixelator 0.19.0 released

· 2 min read

We are releasing a new version of our data processing and analysis library pixelator. Version 0.19.0 comes with major features. Continue reading if you want to stay well informed!

Stable IDs​

Version 0.19 series is now deterministic given the same input across two or more pixelation re-runs with the same version. From now on, if you haven't changed the input files or any parameters, you will get the same cells with the same IDs.

We create this stable IDs by hashing the UPI content of the cells, so if it is the same content, it will be the same ID. Even if cell IDs will look somewhat mangled, they mean something.

Iterative refinement​

We now have incorporated an iterative process that helps us eliminating most of the putative technical doublets in the dataset. We detected this with the help of some customers and it was likely present if you were working with cell lines.

Behaviour of the doublet resolution process, can be fine tuned with --max-refinement-recursion-depth and --max-edges-to-split options. You can learn more about what those parameters mean in our nf-core/pixelator pipeline documentation.

Improved error handling​

Under certain conditions, such as using the wrong panel file in your sample sheet, we might stop the processing of data earlier.

To enable better cell outputs for clinical or partially degraded samples, we have clarified the usage of limits in the cell annotation algorithm we use.

The parameters --min-size and --max-size in the annotate stage should not be used at the same time as --dynamic-filter. And in any case, there is a lowest threshold of 300 molecules in a cell that can be overridden with --min-size.

Multiple Experimental contrasts enabled​

We have listened to your feedback and we are providing you with functionality both in R and Python to do multiple comparisons of your samples for abundance and spatial metrics. This is very useful in cases you are working with multiple conditions or patients and will be demonstrated in one of our advance tutorials in the latest version of the software site.

You can always access and read the more technically detailed release notes for pixelator, for pixelatorR and nf-core/pixelator.