The science behind the suite

If it went into a figure,
it belongs in the methods.

Atlascope is software that computes published numbers, so it should be citable like any other piece of analysis software. Here is the line to copy, and what to put in it.

The short form

Cite the tool, not the suite, because that is what did the work, and always give the version, because these tools change often and a number can move between releases when a divergence is fixed.

Atlascope. <Tool> version <x.y.z>. https://getatlascope.com (accessed <date>).

Where to find the version

Every tool shows its version in its own top bar. The same numbers are listed together in your workspace under Last updates, and in the public changelog, which says what each one changed.

In a methods section

A citation is more useful when it names the method as well as the tool. These are the forms we would write ourselves; the method names come from the methods page.

ELISA standard curves were fitted with a four-parameter logistic model in Sorbet (Atlascope, version <x.y.z>), and concentrations were back-calculated from that fit. Relative expression was computed by the Pfaffl method with measured amplification efficiencies in CtExplorer (Atlascope, version <x.y.z>), normalised to the geometric mean of <reference genes>. Spectral panel design, spillover scoring and titration planning were carried out in CytoMix (Atlascope, version <x.y.z>). Differential expression was run with DESeq2 through LavaSEQ (Atlascope, version <x.y.z>), with Benjamini-Hochberg control of the false discovery rate. Figures and statistics were produced in TwistPlot (Atlascope, version <x.y.z>); the test used is named on each panel.

Cite the underlying method too. If your analysis rests on DESeq2, limma, fgsea, Scanpy or the Pfaffl model, those papers deserve the citation as much as we do, and a reviewer will look for them. They are all listed, with their DOIs, on the methods page.

BibTeX

@misc{atlascope, title = {Atlascope: <Tool>}, author = {{Atlascope}}, year = {2026}, note = {Version <x.y.z>}, howpublished = {\url{https://getatlascope.com}} }

Versions, as of 2026-10-02

These are the versions in production on the day this page was built. Take the one shown in the tool itself if you are writing up work done on another day.

ToolVersionReleased
TwistPlot7.3.0 2026-09-30
Sorbet2.9.2 2026-10-02
CtExplorer6.0.0 2026-10-02
CytoMix7.0.0 2026-10-01
LavaSEQ3.8.2 2026-09-18
FlowFusion2.8.3 2026-09-23
Plaquo6.3.0 2026-10-01
Dizics1.9.8 2026-09-21
Mirage2.2.3 2026-09-27

Is there a DOI?

Not yet. Atlascope has no published paper and no archived release with a DOI, and we would rather say so than point you at something that does not exist. If your journal requires a persistent identifier for software, write to support@getatlascope.com: archiving a tagged release so it gets a DOI is something we can do, and knowing that someone needs it is what would make it happen.

Reproducibility, honestly

Two things are worth knowing before a reviewer asks.

  • The version matters. These tools are in active development. Recording the version you used is what lets anyone, including you, get the same numbers again later.
  • The analysis file is the record. Every tool saves the whole analysis, not just the picture: the data, the roles, the settings and the choices. Keeping that file next to the figure is worth more than any citation, and it opens again in a later version.