Registry
Core assay registry
A registered assay fixes the quantities it measures and the conditions that must be stated for two results to be comparable. A required condition is satisfied by a key of that name in the criterion method conditions object.
Methods
Identifier, measurands, and the conditions each one requires.
| Assay | Fixture | Population | Measures | Required conditions |
|---|---|---|---|---|
| wwd.assay:electrode_impedance_spectroscopy | required | required | wwd:electrode_impedance | frequency, electrolyte, amplitude |
| wwd.assay:flow_cytometry_purity | not required | required | wwd:purity, wwd:viability | marker_panel, gating_strategy, instrument, isotype_control |
| wwd.assay:force_transducer | required | not required | wwd:peak_twitch_force, wwd:tetanic_force, wwd:passive_tension | temperature, stimulation_frequency, stimulation_pulse_width, preload, medium |
| wwd.assay:image_cell_density | not required | required | wwd:seeding_density_areal, wwd:capillary_density | stain, objective, field_area, software |
| wwd.assay:mea_burst_analysis | required | required | wwd:burst_rate, wwd:network_burst_rate, wwd:network_burst_participation | temperature, medium, recording_duration, sampling_rate, filter_band, spike_threshold, burst_detector, burst_parameters |
| wwd.assay:mea_spike_rate | required | required | wwd:mean_firing_rate, wwd:active_electrode_fraction | temperature, medium, recording_duration, sampling_rate, filter_band, spike_threshold |
| wwd.assay:mycoplasma_pcr | not required | not required | wwd:mycoplasma | kit, target, positive_control |
| wwd.assay:optical_contraction_tracking | not required | not required | wwd:unloaded_shortening, wwd:contraction_frequency, wwd:spontaneous_beat_rate, wwd:time_to_peak_force, wwd:half_relaxation_time | temperature, frame_rate, medium, software |
| wwd.assay:pillar_deflection_force | required | not required | wwd:peak_twitch_force, wwd:tetanic_force, wwd:passive_tension | temperature, stimulation_frequency, stimulation_pulse_width, medium |
| wwd.assay:shear_rheometry | not required | not required | wwd:ecm_stiffness, wwd:substrate_modulus | temperature, matrix_concentration, strain_amplitude, frequency |
| wwd.assay:sterility_culture | not required | not required | wwd:microbial_growth | media, incubation_temperature, incubation_duration |
| wwd.assay:structure_tensor_alignment_2d | not required | not required | wwd:fiber_alignment, wwd:cell_alignment | stain, objective, measurement_plane, window_size, software |
| wwd.assay:viability_dye_exclusion | not required | required | wwd:viability | dye, counting_method |
Definitions
What each method measures, as written in the registry.
| Assay | Definition |
|---|---|
| wwd.assay:electrode_impedance_spectroscopy | Electrode impedance magnitude at a stated frequency in a stated electrolyte. |
| wwd.assay:flow_cytometry_purity | Fraction of events in a stated gate for a stated marker panel. |
| wwd.assay:force_transducer | Force measured directly by a calibrated transducer with the construct held at a stated preload. |
| wwd.assay:image_cell_density | Object count per unit area from stained images over stated fields. |
| wwd.assay:mea_burst_analysis | Single-electrode and network burst statistics computed from a spike train by a named detector with stated parameters. |
| wwd.assay:mea_spike_rate | Spike rate from extracellular recordings on a microelectrode array, after a stated filter chain and threshold. |
| wwd.assay:mycoplasma_pcr | Detection of mycoplasma nucleic acid by PCR against a stated target with a stated positive control. |
| wwd.assay:optical_contraction_tracking | Contraction kinematics measured by tracking construct or marker displacement in a video sequence. |
| wwd.assay:pillar_deflection_force | Force inferred from the lateral deflection of a compliant post or pair of posts against which the tissue contracts, multiplied by the post's bending stiffness. |
| wwd.assay:shear_rheometry | Shear storage modulus of a cast gel measured on a rotational rheometer in the linear viscoelastic regime. |
| wwd.assay:sterility_culture | Absence of microbial growth in stated media over a stated incubation period. |
| wwd.assay:structure_tensor_alignment_2d | Planar order parameter obtained from the structure tensor of an image, over a stated evaluation window. |
| wwd.assay:viability_dye_exclusion | Fraction of cells scored viable by exclusion of a membrane-impermeant dye. |
Condition keys
Every condition name used across the registry, and the methods that require it.
| Condition | Methods | Required by |
|---|---|---|
| amplitude | 1 | wwd.assay:electrode_impedance_spectroscopy |
| burst_detector | 1 | wwd.assay:mea_burst_analysis |
| burst_parameters | 1 | wwd.assay:mea_burst_analysis |
| counting_method | 1 | wwd.assay:viability_dye_exclusion |
| dye | 1 | wwd.assay:viability_dye_exclusion |
| electrolyte | 1 | wwd.assay:electrode_impedance_spectroscopy |
| field_area | 1 | wwd.assay:image_cell_density |
| filter_band | 2 | wwd.assay:mea_burst_analysis, wwd.assay:mea_spike_rate |
| frame_rate | 1 | wwd.assay:optical_contraction_tracking |
| frequency | 2 | wwd.assay:electrode_impedance_spectroscopy, wwd.assay:shear_rheometry |
| gating_strategy | 1 | wwd.assay:flow_cytometry_purity |
| incubation_duration | 1 | wwd.assay:sterility_culture |
| incubation_temperature | 1 | wwd.assay:sterility_culture |
| instrument | 1 | wwd.assay:flow_cytometry_purity |
| isotype_control | 1 | wwd.assay:flow_cytometry_purity |
| kit | 1 | wwd.assay:mycoplasma_pcr |
| marker_panel | 1 | wwd.assay:flow_cytometry_purity |
| matrix_concentration | 1 | wwd.assay:shear_rheometry |
| measurement_plane | 1 | wwd.assay:structure_tensor_alignment_2d |
| media | 1 | wwd.assay:sterility_culture |
| medium | 5 | wwd.assay:force_transducer, wwd.assay:mea_burst_analysis, wwd.assay:mea_spike_rate, wwd.assay:optical_contraction_tracking, wwd.assay:pillar_deflection_force |
| objective | 2 | wwd.assay:image_cell_density, wwd.assay:structure_tensor_alignment_2d |
| positive_control | 1 | wwd.assay:mycoplasma_pcr |
| preload | 1 | wwd.assay:force_transducer |
| recording_duration | 2 | wwd.assay:mea_burst_analysis, wwd.assay:mea_spike_rate |
| sampling_rate | 2 | wwd.assay:mea_burst_analysis, wwd.assay:mea_spike_rate |
| software | 3 | wwd.assay:image_cell_density, wwd.assay:optical_contraction_tracking, wwd.assay:structure_tensor_alignment_2d |
| spike_threshold | 2 | wwd.assay:mea_burst_analysis, wwd.assay:mea_spike_rate |
| stain | 2 | wwd.assay:image_cell_density, wwd.assay:structure_tensor_alignment_2d |
| stimulation_frequency | 2 | wwd.assay:force_transducer, wwd.assay:pillar_deflection_force |
| stimulation_pulse_width | 2 | wwd.assay:force_transducer, wwd.assay:pillar_deflection_force |
| strain_amplitude | 1 | wwd.assay:shear_rheometry |
| target | 1 | wwd.assay:mycoplasma_pcr |
| temperature | 6 | wwd.assay:force_transducer, wwd.assay:mea_burst_analysis, wwd.assay:mea_spike_rate, wwd.assay:optical_contraction_tracking, wwd.assay:pillar_deflection_force, wwd.assay:shear_rheometry |
| window_size | 1 | wwd.assay:structure_tensor_alignment_2d |
The condition key fixture is satisfied by a fixture reference on the criterion
rather than by a key in the conditions object.
- The three Core registries.
- The property registry, which defines the measurands above.
- Example packages citing these methods in acceptance criteria.