Design a Flow Cytometry Panel

Design your flow cytometry staining panel where your instruments, your antibody stock, and your acquired controls already live. You lay out markers and fluorochromes, and Conspecta scores every pairing on the cytometer you pick, shows what your lab already owns, and keeps the finished panel as a record your whole team can open and reuse.

Create a Panel

Panels live in the Cytometry workspace, on the Panels tab. New panel takes a name, whether the panel is private or shared, and a first pass at the roster: one line per marker with the dye it rides on. One dye is enough to start, and the markers stay editable afterwards. The panel itself holds a row per marker, with columns for Marker, Fluorochrome, Clone, Titer (µL/test), Stain index, and Notes. The marker and fluorochrome cells drive the checks below. The rest keep the facts a panel spreadsheet usually holds, so the clone and titer travel with the panel instead of living in a file on one person's desktop.

A panel is a project record like any other. Share it with your team, star the ones you reach for, and open the exact panel a run used months later.

Pick the Instrument

The same two dyes can resolve cleanly on one cytometer and collide on another, so a panel is always checked against a machine. Score this panel on picks one: a cytometer from your own lab, or a model from the instrument catalog.

The first machine you pick is the one the panel is bound to. Picking another after that compares instead of committing: every number redraws on the new machine, and a Comparing bar says the panel is still bound to the old one, offering Bind to to keep the new machine and Back to to drop it. You can try a panel on the cytometer down the hall without touching what it was designed on.

Your own machines give the truest answer. Record a cytometer's lasers and detectors on its instrument profile and every panel scored on it uses that exact geometry. A catalog model scores against the manufacturer's typical configuration, and the check says so, because installed filter sets vary from site to site.

Read the Panel Check

The verdict rides in a band across the top of the panel, in the design view and above the worksheet grid alike. Every fluorochrome Conspecta recognizes is scored against every other on the chosen instrument, and the pairs most likely to cost you resolution are flagged on their rows, worst first, so even a wide roster reads at a glance.

Two labels carry the honesty. A name marked not in registry is one Conspecta could not match to a known dye, which is how a typo surfaces instead of silently skipping its checks. A dye marked unscored could not be scored on this instrument, so treat that pairing as unchecked rather than clear. Conspecta never fills a gap with a reassuring number.

The check scores spectral overlap. Titration, controls, and validation at the bench stay yours, and the panel is where you record what they told you.

Open the Worksheet

A panel opens on its design view, which holds the roster, the spectra, and the checks. Open worksheet shows the same panel as the grid it is: one row per marker, one column per field, edited as cells. It is where the clone, the titer, the stain index and the notes get typed, and where you add or reorder rows.

The check rides above the grid the whole time, so a flagged pair stays in front of you while you edit. Design view goes back. Which of the two you are looking at is held in the page address, so a link you send opens on the view you sent.

Score From Your Own Controls

Published spectra are idealized curves. Your acquired single-stain reference controls are what each dye actually does on your machine. Upload reference controls, on the Dye reference, reads the FCS files from a reference run, matches each tube to its dye, and stores the measured signature for that cytometer.

From then on, every panel checked on that machine scores with your measured signatures ahead of the catalog curves, and dyes you compare show a brightness measured from your own control on that instrument, which tells you more than a stain index measured on someone else's.

Explore the Dye Reference

Dye reference on the Panels tab opens the spectra explorer. Search the dye registry, draw emission curves together, add the excitation side with Excitation curves (dashed), and switch instruments to watch the same combination resolve differently on different machines. Dyes your lab already owns are marked, read from the fluorochrome field on your antibody items.

When a combination looks right, Save as panel turns the current selection into a new panel and carries the instrument along with it.

Fill the Next Slot

With a panel and an instrument in place, Best fits for the next slot ranks candidate dyes by what you can reach for. Anything that resolves on the bound instrument without colliding with the panel counts as working, and inside that group your own shelf sets the order: in-date stock first, then expired stock, then dyes you would need to buy. Brightness measured from your controls is shown alongside and is not ranked on.

Once a candidate carries a caveat the list splits in two. Works on this instrument holds the clear ones, and Worth a second look holds the rest, each naming the panel dye it sits close to or crowds, or saying it has no curve to score on. A candidate that crowds something is dimmed rather than dropped, so you can still pick it on purpose. While every candidate is clear the list stays a single plain run.

Each candidate draws its own emission curve against the dyes already on the panel, over the same wavelength range for every row, so you can see where it lands and whether it overlaps anything before reading a word. Point at a row, or tab to it, and that candidate also draws on the panel's spectra chart above, dashed and named, so the same look places it across the whole range.

Open a marker from the roster and the same ranking sits beside its Marker and Fluorochrome fields as Best fits for this slot. The ranking reads the panel's remaining spectral room and your shelf, so it holds for whichever marker the slot ends up carrying. Once the row has a dye, that space becomes its Dye fit verdict: the worst pairs it collides with and its slice of the similarity matrix. Swap dye opens the ranked candidates in a picker. On a phone the two stack, fields first.

The order comes from the spectra and your own inventory, never from a vendor. You stay the designer. Suggestions exist so your next candidate comes from a shortlist instead of a catalog.

Export the Panel

Export sits in the band at the top of a panel and on the strip above the worksheet, so a file is one click from either view. Which of the three you want depends on who is going to read it.

The three files that carry the matrix carry its caveats with it, written above the numbers. Which instrument the scores were computed on, whether your own reference controls were used or published curves, which dyes could not be scored, and the two thresholds that turn a number into a flag. A panel checked with no instrument bound says so in its first line, so a matrix opened months later on someone else's computer still says what it is worth.

The panel sheet asks for a Width in millimetres and a Resolution, the same way a figure does, so a picture bound for a slide and one bound for print come out at the sizes each needs. The dialog box shows the pixel dimensions your choices produce before you write the file.

Project members with view-only access can export a panel, the same as they can open one.

Hand the Panel to a Client Lab

A panel a core facility designs is usually run for another lab. Sharing works at the project level, so give the engagement its own project, then add the client's scientists to it with View only, the same way you bring in any outside collaborator. They see that project's work and only that project's work, and the panel they open is always the current version, so every revision you make reaches them the moment you save it. What was designed, on which cytometer, with which clones and titers, stays one living record.

For a client who works outside Conspecta, Export writes that record as a file. The workbook carries the roster, the cytometer it was designed for, and the checks, which is what a collaborator needs to run the panel or to write it up.