check_flow_cytometry_quality
Read-only
Acquisition quality over time for an FCS file, by flowAI (flow rate, signal acquisition and dynamic range checks), PeacoQC (peak trajectories, isolation tree and MAD) or flowCut (deviant and low-density segments).
Tool call template
This tool declares no required parameters. Add optional parameters from the input schema as needed.
{
"id": 1,
"jsonrpc": "2.0",
"method": "tools/call",
"params": {
"arguments": {},
"name": "check_flow_cytometry_quality"
}
}Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| A | No | additional negative decades. Only applies when scale is logicle or hyperlog or flowcore-logicle or fasinh. | |
| M | No | decades of the full scale. Only applies when scale is logicle or hyperlog or flowcore-logicle or fasinh. | |
| T | No | top of scale; empty means the file's largest fluorescence $PnR. | |
| W | No | linear width in decades. Only applies when scale is logicle or hyperlog or flowcore-logicle. | |
| tool | No | the method. Values: flowai (flowAI), peacoqc (PeacoQC), flowcut (flowCut). | flowai |
| scale | No | the display scale of the fluorescence channels (scatter and time stay linear): used for the plot, the threshold and, with `stats_on: scaled`, the statistics. Values: logicle (Logicle (Gating-ML 2.0, Moore & Parks)), fasinh (ArcSinh (Gating-ML 2.0 fasinh)), arcsinh (ArcSinh with a cofactor (asinh(x / c), Cytobank and CyTOF)), hyperlog (Hyperlog (Gating-ML 2.0, Bagwell)), flowcore-logicle (Logicle on a 0–M axis (flowCore)), wsp-biex (Biex (FlowJo 10, channels 0–4096)), flin (Linear (Gating-ML flin)). | logicle |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| gating | No | a Gating-ML 2.0 document in the project, by name or id; empty for no gating (every statistic is then of all events). | |
| plot_x | No | channel (PnN or PnS) on the density plot's x axis; empty for no plot. | |
| plot_y | No | channel on the plot's y axis. | |
| derived | No | derived parameters, `name = expression` separated by `;` (FlowJo's vocabulary: channels by name or [name], + − * / % ^, abs ceil floor neg round max min pow exp ln log sqrt and the trig functions); each becomes a channel of the run. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| cofactor | No | the c in asinh(x / c): 5 is the CyTOF convention, 150 a common one for fluorescence. Only applies when scale is arcsinh. | |
| document | No | the FCS file, by name or id; may be left empty when the project holds exactly one. | |
| peaco_mad | No | PeacoQC MAD. Only applies when tool is peacoqc. | |
| biex_width | No | FlowJo biex width basis (negative; FlowJo's default -10). Only applies when scale is wsp-biex. | |
| compensation | No | `auto`: the file's own $SPILLOVER/$SPILL when it has one, else none; `file`: that, refusing a file without one; `none`: leave the values as acquired. Values: auto (automatic), file (file's own matrix), none (none). | auto |
| biex_negative | No | FlowJo biex extra negative decades. Only applies when scale is wsp-biex. | |
| peaco_it_limit | No | PeacoQC isolation tree limit. Only applies when tool is peacoqc. | |
| flowcut_segment | No | flowCut segment (events). Only applies when tool is flowcut. | |
| plot_population | No | the population plotted; empty for all events. | |
| peaco_consecutive | No | PeacoQC consecutive bins. Only applies when tool is peacoqc. | |
| flowai_remove_from | No | flowAI: which checks remove events. Only applies when tool is flowai. | all |
| compensation_method | No | which published algorithm: FlowKit's solve(Sᵀ, Xᵀ) or flowCore's X · S⁻¹. They agree to ~1e-15 of full scale. Values: flowkit (solve(Sᵀ, Xᵀ) (FlowKit)), flowcore (X · S⁻¹ (flowCore)). Only applies when compensation is auto or file. | flowkit |
| flowcut_max_perc_cut | No | flowCut MaxPercCut. Only applies when tool is flowcut. | |
| flowcut_max_valley_hgt | No | flowCut MaxValleyHgt. Only applies when tool is flowcut. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| kept | Yes | events kept | |
| table | Yes | the method's own result table | |
| causes | Yes | per cause: events flagged, whether it removes, and flagged events per time bin | |
| channels | Yes | the per-channel table (changepoints, MAD contribution, margins) |