Flow cytometry analysis in your browser

FlowJo has been the default flow cytometry analysis tool for decades, and for good reason. The friction usually isn't the analysis itself, it's everything around it. There's a per-seat license to renew, a desktop app to install and update on every machine as new versions ship, and analysis that lives in workspace files passed from one person to the next. For a lab that mostly needs to gate a few panels, compensate, and pull clean statistics, that overhead is the part worth shedding.

Conspecta moves the same everyday workflow into the browser. You open an FCS file, draw gates, apply a compensation matrix, and run t-SNE or SOM clustering without installing anything or holding a seat. Because it's a browser tool, the researcher on a Mac, the student on a Chromebook, and the PI reviewing on a tablet all open the same link and see the same analysis.

The clearest difference isn't in the gating, it's in what happens after. FlowJo analyzes the FCS file in front of it and leaves the rest to you. The sample it came from, the timepoint, the genotype, and the figure it ends up in all live in other tools. In Conspecta, a gated population stays attached to the sample it was measured from, so its timepoint, condition, and genotype travel with it, and a figure you build pulls straight from that analysis.

In practice that means less of the manual bookkeeping that causes mistakes. You aren't exporting statistics into a spreadsheet, relabeling wells, and pasting plots into a separate figure tool, so there's less chance of a mislabeled condition or a figure built from a stale export. The flow work sits in the same project as the samples, images, and notebook it relates to.

Moving over is mostly a one-time step. Upload your FCS files, then open your FlowJo 10 workspace with Import gating. Conspecta reads the `.wsp` in your browser, rebuilds the gating strategy, runs it over your own files, and shows its count beside FlowJo's for every population, so you can see how closely they agree before you keep anything. Populations it can't rebuild are listed and marked, never quietly dropped.

Rectangle, polygon, ellipse, quadrant, range, and boolean gates all come across. Ellipses are rebuilt exactly as the workspace states them, so FlowJo's own count can sit a fraction of a percent away, because FlowJo counts events through a slightly grown, screen-resolution copy of its own ellipse. Two things genuinely can't be rebuilt, and Conspecta names them rather than guessing: curly-quadrant gates, which have no equivalent outside FlowJo, and a gate on a marker a spectral instrument never stored, because the workspace derives it from the raw detector channels.

From there you save the strategy as a template the whole team gates from, rather than passing a workspace file around. It leaves the same way it arrived: results as FCS, Excel, or CSV, and the strategy itself as ISAC Gating-ML 2.0 or a FlowJo 10 .wsp, so a collaborator who stays on FlowJo opens your gating directly and nothing you do is locked into the tool.