Recruitment: compartment ratios and channel identity

From Home → Organism → Toxoplasma, open Recruitment after segmentation and measurement. Supply the project containing measurements/measurements.db and verify that its cell, nucleus, pathogen and cytoplasm measurements refer to the intended objects and channels. See Recruitment in the module map and spacr.submodules.analyze_recruitment() for the surrounding workflow.

For whole-vacuole marker states, explicit host infection denominators and optional parasite counts, see Host–Pathogen Analysis. The two modules remain separate analysis choices.

Select channel_of_interest for the fluorescent marker whose recruitment you want to measure. Each row is one host cell: the mean intensities of the pathogen objects assigned to that cell are averaged, and the primary recruitment column divides that pathogen mean by the cell’s cytoplasm mean intensity in the same channel. Configure the condition metadata, object size/intensity filters and minimum objects per well before comparing results. Inspect compartment identities and denominator intensities; an absent or zero denominator does not establish recruitment.

Auxiliary ratios retain their channel

channel_dims selects image-channel indices for overlays and auxiliary recruitment measurements. The auxiliary calculation also includes channel_of_interest if it was omitted from that list. Output names follow this pattern:

pathogen_channel_<channel>_<compartment>_<statistic>_ratio

compartment is cell, cytoplasm or nucleus. Each denominator is the mean intensity of that compartment in the same channel. statistic identifies the pathogen numerator:

Statistic	Measurement used as numerator
mean	pathogen_channel_<channel>_mean_intensity
q75	pathogen_channel_<channel>_percentile_75
outside_mean	pathogen_channel_<channel>_outside_mean
outside_q75	pathogen_channel_<channel>_outside_percentile_75
periphery_mean	pathogen_channel_<channel>_periphery_mean

For example, a channel 2 pathogen mean of 12 and cytoplasm mean of 4 produces pathogen_channel_2_cytoplasm_mean_ratio = 3. If channel 3 has means of 100 and 4, its separate column is pathogen_channel_3_cytoplasm_mean_ratio = 25. Calculating channel 3 retains the channel 2 result. These are illustrative intensities, not experiment data.

The calculation produces fifteen auxiliary ratios per channel. It does not create constant-one pathogen/nucleus slope columns; these ratios do not estimate a spatial slope. Genuine slope columns already supplied by the caller are preserved. When comparing historical exports, check whether their auxiliary column names identify a channel before combining runs.

Saved results

The run writes results/cells.csv with the retained per-host-cell rows and results/wells.csv with per-well means of those rows, alongside recruitment plots. Rows in cells.csv combine all pathogen objects assigned to a host cell; they are not independent per-vacuole measurements. For measurements linked to individual vacuoles, use Host–Pathogen Analysis. Verify condition assignments, filtering and the selected channel when comparing these two aggregation levels.