Troubleshooting

The download is blocked

Microsoft Edge refuses the installer. Use Firefox or Chrome. Edge blocks these files and its message can look like the file is unavailable rather than blocked. See Install.

A script or curl gets rejected. The filenames contain a space; the URL must be percent-encoded (%20).

Windows says the publisher is unknown

Expected on a new product. The installer is signed — SmartScreen reputation accrues with install volume and a recent release has not accrued it yet. More info → Run anyway. See Install.

My license file does not appear in the picker

Older builds filtered the file picker to .json only, which made a license with a different extension invisible rather than rejected — nothing to click and no explanation.

Rename the file so it ends in .json. The extension is cosmetic; the app verifies the contents and the signature, not the name. Current builds accept both extensions and offer an all-files option.

Gating, export or AI is refused

That is the license boundary. Viewing always works; editing, exporting and AI need an active license. The message names which of the three was blocked and whether the license has expired or was never installed — read it rather than guessing, because “expired” and “never heard of you” need different fixes.

A population is smeared against the axis, or has vanished

Almost always the scale, not the gate and not the compensation.

Compensated data contains negative values. A log axis cannot display them, so a real negative population piles against the axis or disappears. Switch that axis to logicle, asinh or hyperlog.

AI-1 declines everything, or declines a population I clearly have

Check channel names first. AI-1 identifies channels by the marker they measure, not by fluorochrome or channel order — a channel called FL4-A with no marker name is invisible to it. Name your markers in the parameter editor and run it again.

If names are right and it still declines, read the competence report. Three distinct things cause a decline, and they need different responses:

• The marker is not in the panel — nothing to do; the call is not possible.
• The population is out of repertoire — AI-1 covers a published list, human samples only. Gate it by hand or use the copilot.
• The data looks unfamiliar — a different instrument or protocol than it was trained on. Its ranking may still be useful but its thresholds are not calibrated for your data.

Also confirm the sample is human. On mouse data the model separates populations well and calibrates disastrously, which is exactly why it refuses rather than reporting a number.

Statistics are not what I expect

Check what the percentage is a percentage of. A population’s frequency is a percentage of its parent, not of all events. Look at the breadcrumb above the plot and the population’s place in the hierarchy. See Statistics.

A workspace opens with missing files

The workspace references your FCS files rather than copying them, so moving or renaming the data breaks the link. The app asks you to relocate them. See Workspaces.

Compensation looks wrong after I changed it

Gates are regions in a coordinate space. Change the compensation underneath and the events inside a gate can change. Compensate first, then gate — and if you must change it afterwards, check every gate. See Compensation.

A large file is slow

A million events is normal and takes roughly a minute and a half on a typical laptop. Substantially slower than that is worth reporting, with the event count and your machine’s specification.

Still stuck

Help → Report an Issue. It sends the version, your platform, your license tier and your description. No screenshots and nothing from your data files — file paths and data filenames are stripped from your description before it is sent, because sample identifiers live in filenames.

If we need a screenshot or a sample to reproduce something, we ask you directly and tell you what is safe to send.

If the reporter itself cannot reach us — the machine is offline, or a licensing problem is blocking it — email [email protected] with your version number (Help → About Cytogence) and what you were doing.