Interpreting cytometry outputs
FlowSOM cluster assignments, segmentation masks, and spatial interaction scores.
cytometryoutputs
Retired tools
flow_gate, flow_cluster and flow_differential are retired and their outputs are no longer produced. For FCS clustering use flowsom. There is no hosted tool for automated gating or differential abundance; ask Ivy to run those in Python in the chat's code workspace.
Each tool returns discovered clusters, segmentation masks, or spatial interaction scores. Use them to map cell populations and cell neighborhoods, and to export the results for downstream analysis.
Documented output fields go beyond the implemented tools
The IMC field tables below describe the intended result shape; the registered IMC backends currently return a much smaller set of fields.
Interpreting cytometry outputs
FlowSOM output
flowsom returns:
- SOM information: the grid dimensions (
xdim,ydim) and training time. - A metacluster summary: the size and fraction of events in each metacluster, and which SOM nodes belong to it.
- Per-metacluster median marker intensities (MFIs), and per-node MFIs.
- Per-event cluster labels as a CSV.
- An optional star plot PNG of the SOM grid (
generate_plot).
IMC Segment output
| Field | Type | Description |
|---|---|---|
total_cells | number | Total cells segmented |
method | string | Segmentation method used |
image_dimensions | object | Image width and height in pixels |
pixel_size | number | Pixel size in microns |
cell_mask | file | Cell mask image (TIFF, each cell labeled with unique integer) |
cell_data | file | CSV with per-cell features |
segmentation_stats | object | Quality metrics |
Cell data fields
| Field | Type | Description |
|---|---|---|
cell_id | integer | Unique cell identifier (matches mask label) |
x_centroid | number | X coordinate of cell centroid (microns) |
y_centroid | number | Y coordinate of cell centroid (microns) |
area | number | Cell area in square microns |
eccentricity | number | Cell shape eccentricity (0 = circle, 1 = line) |
solidity | number | Cell boundary regularity (0-1, higher = smoother) |
marker_* | number | Mean intensity of each marker within the cell mask |
Segmentation quality metrics
| Field | Type | Description |
|---|---|---|
mean_cell_area | number | Mean cell area in square microns |
median_cell_area | number | Median cell area |
std_cell_area | number | Standard deviation of cell area |
oversegmentation_rate | number | Estimated rate of split cells (0-1) |
undersegmentation_rate | number | Estimated rate of merged cells (0-1) |
cells_per_mm2 | number | Cell density |
IMC Spatial output
| Field | Type | Description |
|---|---|---|
analysis_type | string | Analysis type performed |
total_cells | number | Total cells analyzed |
cell_types_analyzed | string[] | Cell types included |
radius | number | Neighborhood radius (microns) |
permutations | number | Number of permutations for significance |
results | object | Analysis-specific results |
Neighborhood analysis fields
| Field | Type | Description |
|---|---|---|
interactions | array | Pairwise cell type interaction results |
Interaction fields
| Field | Type | Description |
|---|---|---|
cell_type_a | string | First cell type |
cell_type_b | string | Second cell type |
observed_frequency | number | Observed interaction frequency |
expected_frequency | number | Expected frequency under random spatial distribution |
interaction_score | number | Ratio of observed to expected (>1 = attraction, <1 = avoidance) |
z_score | number | Z-score from permutation testing |
p_value | number | Permutation p-value |
relationship | string | "attraction", "avoidance", or "random" |
Interaction score interpretation
| Score | Z-score | Interpretation |
|---|---|---|
| > 2.0 | > 3.0 | Strong spatial attraction |
| 1.5 - 2.0 | 2.0 - 3.0 | Moderate attraction |
| 0.7 - 1.5 | -2.0 - 2.0 | Random spatial distribution |
| 0.3 - 0.7 | -3.0 - -2.0 | Moderate avoidance |
| < 0.3 | < -3.0 | Strong spatial avoidance |
Spatial statistics fields
| Field | Type | Description |
|---|---|---|
ripleys_k | object | Ripley's K function values at multiple radii |
ripleys_l | object | Ripley's L function (variance-stabilized K) |
nearest_neighbor | object | Nearest-neighbor distance distributions per cell type |
morans_i | object | Moran's I spatial autocorrelation per marker |
Community detection fields
| Field | Type | Description |
|---|---|---|
n_communities | number | Number of spatial communities identified |
communities | array | Community descriptions |
Community fields
| Field | Type | Description |
|---|---|---|
community_id | string | Community identifier |
n_cells | number | Number of cells in this community |
dominant_types | object | Cell type composition (type -> frequency) |
spatial_extent | number | Approximate diameter in microns |
description | string | Suggested tissue microenvironment label |
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