Add BD FACSMelody cell sorter support#1156
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Introduce a CellSorter (FACS) capability and a BD FACSMelody backend that implements it, so a deck can run sort-to-plate as a normal device call. This closes the one step in plate-based single-cell sequencing that usually has to happen off-automation, and enables sorting for a target population before an assay (cell-type resolution for downstream measurements). Capability (pylabrobot/capabilities/cell_sorting): - CellSorter frontend with validation and a sort_to_plate convenience method - CellSorterBackend ABC (get_status, load_template, set_deposition, prime, start_sort, wait_for_completion, abort, clean) - CellSorterChatterboxBackend for device-free testing - Designed to sit alongside a future cytometry capability sharing the same fluidics and gate-template primitives BD FACSMelody backend (pylabrobot/becton_dickinson/facsmelody): - FACSMelodyDriver: the guarded wire. Dry-run by default; refuses to actuate without an explicit opt-in and refuses a live run against an incomplete ProtocolMap - FACSMelodyCellSorterBackend: turns CellSorter operations into decoded frames - Consumer-side ProtocolMap loader (the RE toolkit that produces the map stays in an external repo and is not vendored) - Not yet hardware-validated; labeled untested until a bench run Docs: a cell-sorting capability page and a FACSMelody reverse-engineering playbook (docs/facsmelody-re.md) following the established PyLabRobot method. Tests: device-free coverage of the capability sequencing, argument validation, the actuation guard, and the incomplete-map refusal.
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Heads up on the red checks: they're pre-existing on This PR's additions pass: all |
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thanks for the PR! were you able to verify this on the machine? In yesterday's issue you said that was a todo. If there's anything I can look at in the meantime lmk
yes exactly, dont worry about it :) |
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Not yet, still todo. Melody + plate sort are here, so next is decoding the ProtocolMap off FACSChorus, then guarded replay to a real sort-to-plate. Does CellSorter fit how you'd want a sorter capability in v1b1 (the interface + where it lives)? |
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Why: the science this unlocks
Sorting is the one step in plate-based single-cell sequencing that usually has to
happen off-automation. A liquid handler can build libraries end to end, but the
sort itself, one gated cell per well or a targeted, enriched population, is
typically a manual hand-off. Bringing the sorter under PyLabRobot closes that gap:
the deck stages the plate, calls
sort_to_plate, and finishes the prep. Walkawaylibrary prep becomes possible.
It also enables sorting for a target population: enrich a cell type, a
marker-positive subset, or live singlets before the assay. That is what gives
cell-type resolution to downstream measurements, for example cell-type-specific
epigenomics, where you want to read regulatory state in the exact cell type a
variant acts in rather than in a bulk average.
What this adds
A
CellSorter(FACS) capability and a BD FACSMelody backend that implements it.Capability (
pylabrobot/capabilities/cell_sorting/)CellSorterfrontend: validation plus asort_to_plateconvenience method thatsequences load-template, deposition, prime, sort, wait, clean.
CellSorterBackendABC:get_status,load_template,set_deposition,prime,start_sort,wait_for_completion,abort,clean.CellSorterChatterboxBackendfor device-free testing.BD FACSMelody (
pylabrobot/becton_dickinson/facsmelody/), mirroring thethermo_fisher/cytomat/layout:FACSMelodyDriver: the wire. Loads a decodedProtocolMapand sends framesbehind two independent safety switches.
FACSMelodyCellSorterBackend: turnsCellSorteroperations into the frames themap names.
ProtocolMaploader. The reverse-engineering toolkit thatproduces the map lives in a separate repo and is intentionally not vendored
here; only the read side ships.
Docs: a cell-sorting capability page and a FACSMelody reverse-engineering
playbook (
docs/facsmelody-re.md) that follows the PyLabRobot method (work to theOEM command layer, sniff OEM-to-device traffic, correlate action to bytes, decode
framing, guarded replay over PyUSB/pyserial).
Safety and labeling
The Melody is a laser plus pressurized fluidics, so the backend is conservative by
default:
armed and the call is live.
explicit opt-in; otherwise they raise.
ProtocolMap, so a half-mappedprotocol cannot drive hardware.
hand and will validate sort-to-plate; the code is labeled untested until then.
Per-parameter byte encoders and response parsing are resolved during that
validation, gated behind the coverage check so an unresolved map cannot run live.
The capability is kept small and event-oriented so a cytometry/acquisition
capability can reuse the same fluidics and gate-template primitives later; sorting
and acquisition stay separable so the interface can be aligned before either lands.
Testing
Device-free tests cover the capability sequencing, argument validation, the
actuation guard, and the incomplete-map refusal.
ruff(format + check),mypy,and the new tests pass locally.