| acquisition_datetime |
The datetime of the acquisition |
| acquisition_protocol |
The protocol used to acquire the dataset |
| alpha |
The alpha value of the color (optional) |
| analyzed_bead_centers |
The centers of the beads that have been analyzed |
| array_data |
A non-required slot for non-serializable array data object |
| author |
The author of the comment |
| authors |
The authors of the protocol |
| average_bead |
The average bead image created from all the beads considered valid |
| average_bead_fit_r2_x |
Average coefficient of determination (R^2) for the fits in the X axis of the ... |
| average_bead_fit_r2_y |
Average coefficient of determination (R^2) for the fits in the Y axis of the ... |
| average_bead_fit_r2_z |
Average coefficient of determination (R^2) for the fits in the Z axis of the ... |
| average_bead_fwhm_lateral_asymmetry_ratio |
Lateral FWHM asymmetry ratio for the average bead |
| average_bead_fwhm_micron_x |
FWHM for the average bead in the X axis in microns |
| average_bead_fwhm_micron_y |
FWHM for the average bead in the Y axis in microns |
| average_bead_fwhm_micron_z |
Average FWHM for the beads in the Z axis in microns |
| average_bead_fwhm_pixel_x |
FWHM for the average bead in the X axis in pixels |
| average_bead_fwhm_pixel_y |
FWHM for the average bead in the Y axis in pixels |
| average_bead_fwhm_pixel_z |
FWHM for the average bead in the Z axis in pixels |
| average_bead_intensity_integrated |
Integrated intensity for the average bead |
| average_bead_intensity_max |
Maximum intensity for the average bead |
| average_bead_intensity_min |
Minimum intensity for the average bead |
| average_bead_intensity_std |
Standard deviation of the intensity for the average bead |
| axis |
The axis of the orthogonal image |
| b |
The blue value of the color |
| bead_diameter_micron |
The diameter of the beads in the sample measured in microns |
| bead_profiles_x |
The intensity profiles along the x axis of the analyzed beads as well as the ... |
| bead_profiles_y |
The intensity profiles along the y axis of the analyzed beads as well as the ... |
| bead_profiles_z |
The intensity profiles along the z axis of the analyzed beads as well as the ... |
| bead_properties |
Properties associated with the analysis of the beads |
| bit_depth |
Detector bit depth |
| bottom_center_intensity_mean |
The mean intensity of the bottom-center of the image |
| bottom_center_intensity_ratio |
The mean intensity of the bottom-center of the image divided by the maximum ... |
| bottom_left_intensity_mean |
The mean intensity of the bottom-left of the image |
| bottom_left_intensity_ratio |
The mean intensity of the bottom-left of the image divided by the maximum in... |
| bottom_right_intensity_mean |
The mean intensity of the bottom-right of the image |
| bottom_right_intensity_ratio |
The mean intensity of the bottom-right of the image divided by the maximum i... |
| c |
The c coordinate |
| center_fitted_distance_relative |
The relative distance of the fitted center of illumination to the center of t... |
| center_fitted_x |
The x coordinate of the fitted center of illumination |
| center_fitted_x_relative |
The relative x position of the fitted center of illumination |
| center_fitted_y |
The y coordinate of the fitted center of illumination |
| center_fitted_y_relative |
The relative y position of the fitted center of illumination |
| center_geometric_distance_relative |
The relative distance of the geometric center to the center of the image |
| center_geometric_x |
The x coordinate of the geometric center of the center of illumination region |
| center_geometric_x_relative |
The relative x position of the geometric center of the center of illumination... |
| center_geometric_y |
The y coordinate of the geometric center of the center of illumination region |
| center_geometric_y_relative |
The relative y position of the geometric center of the center of illumination... |
| center_of_mass_distance_relative |
The relative distance of the centers of mass to the center of the image |
| center_of_mass_x |
The x coordinate of the center of mass of the center of illumination region |
| center_of_mass_x_relative |
The relative x position of the center of mass of the center of illumination r... |
| center_of_mass_y |
The y coordinate of the center of mass of the center of illumination region |
| center_of_mass_y_relative |
The relative y position of the center of mass of the center of illumination r... |
| center_region_area_fraction |
The fraction of the area occupied by the center of illumination region |
| center_region_intensity_fraction |
The fraction of the upper intensity range occupied by the center of illuminat... |
| channel_id |
The channel id to which the measurements apply |
| channel_name |
The channel name to which the measurements apply |
| channel_nr |
The channel number to which the measurements apply |
| channel_series |
A series representing channels for multi-channel images |
| channels |
The channels of the ChannelSeries |
| columns |
The columns of the table |
| comment |
A human readable comment |
| comment_collection |
A collection of comments |
| comment_type |
The type of the comment |
| comments |
A list of comments linked to the microscope |
| considered_axial_edge_count |
Number of beads considered as being too close to the top and or bottom of the... |
| considered_bad_fit_x_count |
Number of beads considered as having a bad fit quality in the x axis |
| considered_bad_fit_y_count |
Number of beads considered as having a bad fit quality in the y axis |
| considered_bad_fit_z_count |
Number of beads considered as having a bad fit quality in the z axis |
| considered_bead_centers_axial_edge |
The centers of the beads detected but considered as too close to the top and ... |
| considered_bead_centers_intensity_outlier |
The centers of the beads detected but considered as being too intense and pot... |
| considered_bead_centers_lateral_edge |
The centers of the beads detected but considered as too close to the edge of ... |
| considered_bead_centers_self_proximity |
The centers of the beads detected but considered as too close to another bead |
| considered_bead_centers_x_fit_quality |
The centers of the beads detected but considered as the fit quality in x was ... |
| considered_bead_centers_y_fit_quality |
The centers of the beads detected but considered as the fit quality in y was ... |
| considered_bead_centers_z_fit_quality |
The centers of the beads detected but considered as the fit quality in z was ... |
| considered_intensity_outlier_count |
Number of beads considered as being too intense and potentially represent a c... |
| considered_lateral_edge_count |
Number of beads considered for being too close to the edge of the image |
| considered_self_proximity_count |
Number of beads considered for being too close to another bead |
| considered_valid_count |
Number of beads analyzed |
| corner_fraction |
Input parameter: the proportion of the image to be considered as corner or ce... |
| data_reference |
A reference to the data |
| data_type |
The data type of the column |
| data_uri |
The URI of the object data |
| dataset_class |
The class of the datasets in the collection |
| dataset_collection |
The datasets of the collection |
| datetime |
The datetime to which the comment is referring |
| description |
A human readable description of an entity |
| ellipses |
A list of ellipses included in the ROI |
| emission_wavelength_nm |
The emission wavelength in nm |
| errors |
The errors of the processing by microscope-metrics |
| excitation_wavelength_nm |
The excitation wavelength in nm |
| experimenter |
The experimenter that performed the imaging experiment |
| field_illumination_images |
Input parameter: homogeneity image provided in the order TZYXC |
| fill_color |
The fill color of the shape |
| fit_r2_x_mean |
Mean coefficient of determination (R^2) in the x axis for the analyzed beads |
| fit_r2_x_median |
Median coefficient of determination (R^2) in the x axis for the analyzed bead... |
| fit_r2_x_std |
Standard deviation of the coefficient of determination (R^2) in the x axis fo... |
| fit_r2_y_mean |
Mean coefficient of determination (R^2) in the y axis for the analyzed beads |
| fit_r2_y_median |
Median coefficient of determination (R^2) in the y axis for the analyzed bead... |
| fit_r2_y_std |
Standard deviation of the coefficient of determination (R^2) in the y axis fo... |
| fit_r2_z_mean |
Mean coefficient of determination (R^2) in the z axis for the analyzed beads |
| fit_r2_z_median |
Median coefficient of determination (R^2) in the z axis for the analyzed bead... |
| fit_r2_z_std |
Standard deviation of the coefficient of determination (R^2) in the z axis fo... |
| fitting_r2_threshold |
Threshold for the coefficient of determination (R^2) of the fit to be conside... |
| fwhm_lateral_asymmetry_ratio_mean |
Mean lateral FWHM asymmetry ratio for the analyzed beads |
| fwhm_lateral_asymmetry_ratio_median |
Median lateral FWHM asymmetry ratio for the analyzed beads |
| fwhm_lateral_asymmetry_ratio_std |
Standard deviation of the lateral FWHM asymmetry ratio for the analyzed beads |
| fwhm_micron_x_mean |
Mean FWHM for the analyzed beads in the X axis in microns |
| fwhm_micron_x_median |
Median FWHM for the analyzed beads in the X axis in microns |
| fwhm_micron_x_std |
Standard deviation of the FWHM for the analyzed beads in the X axis in micron... |
| fwhm_micron_y_mean |
Mean FWHM for the analyzed beads in the Y axis in microns |
| fwhm_micron_y_median |
Median FWHM for the analyzed beads in the Y axis in microns |
| fwhm_micron_y_std |
Standard deviation of the FWHM for the analyzed beads in the Y axis in micron... |
| fwhm_micron_z_mean |
Mean FWHM for the analyzed beads in the Z axis in microns |
| fwhm_micron_z_median |
Median FWHM for the analyzed beads in the Z axis in microns |
| fwhm_micron_z_std |
Standard deviation of the FWHM for the analyzed beads in the Z axis in micron... |
| fwhm_pixel_x_mean |
Mean FWHM for the analyzed beads in the X axis in pixels |
| fwhm_pixel_x_median |
Median FWHM for the analyzed beads in the X axis in pixels |
| fwhm_pixel_x_std |
Standard deviation of the FWHM for the analyzed beads in the X axis in pixels |
| fwhm_pixel_y_mean |
Mean FWHM for the analyzed beads in the Y axis in pixels |
| fwhm_pixel_y_median |
Median FWHM for the analyzed beads in the Y axis in pixels |
| fwhm_pixel_y_std |
Standard deviation of the FWHM for the analyzed beads in the Y axis in pixels |
| fwhm_pixel_z_mean |
Mean FWHM for the analyzed beads in the Z axis in pixels |
| fwhm_pixel_z_median |
Median FWHM for the analyzed beads in the Z axis in pixels |
| fwhm_pixel_z_std |
Standard deviation of the FWHM for the analyzed beads in the Z axis in pixels |
| g |
The green value of the color |
| h |
The height |
| image_id |
The id of the image where the measurement was taken |
| image_name |
The name of the image where the measurement was taken |
| input_data |
The input data for the analysis |
| input_parameters |
The input parameters for the analysis |
| integration_time_ms |
The integration time in milliseconds |
| intensity_integrated_mean |
Mean integrated intensity of the analyzed beads |
| intensity_integrated_median |
Median integrated intensity of the analyzed beads |
| intensity_integrated_std |
Standard deviation of the integrated intensity of the analyzed beads |
| intensity_max_mean |
Mean maximum intensity of the analyzed beads |
| intensity_max_median |
Median maximum intensity of the analyzed beads |
| intensity_max_std |
Standard deviation of the maximum intensity of the analyzed beads |
| intensity_min_mean |
Mean minimum intensity of the analyzed beads |
| intensity_min_median |
Median minimum intensity of the analyzed beads |
| intensity_min_std |
Standard deviation of the minimum intensity of the analyzed beads |
| intensity_profiles |
Intensity profiles for the field illumination analysis in the different direc... |
| intensity_profiles_table |
Linked table of profiles |
| intensity_robust_z_score_threshold |
Threshold for the robust z-score of the intensity of the bead to be considere... |
| intensity_std_mean |
Mean standard deviation of the intensity of the analyzed beads |
| intensity_std_median |
Median standard deviation of the intensity of the analyzed beads |
| intensity_std_std |
Standard deviation of the standard deviation of the intensity of the analyzed... |
| is_open |
Is the polygon open |
| key_measurements |
Key measurements is a table summarizing the most important measurements as a... |
| light_source |
The light source under investigation |
| linearity |
The linearity of the power measurements |
| lines |
A list of lines included in the ROI |
| linked_references |
A list of linked references |
| manufacturer |
A manufacturer |
| mask |
The mask image |
| masks |
A list of masks included in the ROI |
| max_intensity |
The maximum intensity of the center of illumination |
| max_intensity_distance_relative |
The relative distance of the maximum intensity to the center of the image |
| max_intensity_pos_x |
The x coordinate of the maximum intensity of the center of illumination |
| max_intensity_pos_x_relative |
The relative x position of the maximum intensity of the center of illuminatio... |
| max_intensity_pos_y |
The y coordinate of the maximum intensity of the center of illumination |
| max_intensity_pos_y_relative |
The relative y position of the maximum intensity of the center of illuminatio... |
| measurement_device |
The power meter used to measure the power |
| measurements_table |
Linked table of measurements |
| microscope |
The microscope that was used to acquire the dataset |
| microscope_collection |
The microscopes of the collection |
| microscope_type |
The type of the microscope |
| middle_center_intensity_mean |
The mean intensity of the middle-center of the image |
| middle_center_intensity_ratio |
The mean intensity of the middle-center of the image divided by the maximum ... |
| middle_left_intensity_mean |
The mean intensity of the middle-left of the image |
| middle_left_intensity_ratio |
The mean intensity of the middle-left of the image divided by the maximum in... |
| middle_right_intensity_mean |
The mean intensity of the middle-right of the image |
| middle_right_intensity_ratio |
The mean intensity of the middle-right of the image divided by the maximum i... |
| min_lateral_distance_factor |
Minimal distance that has to separate laterally the beads represented as the ... |
| model |
The model of a device |
| name |
The human readable name of an entity |
| omero_host |
The host of the OMERO server |
| omero_object_id |
The ID of the OMERO object |
| omero_object_type |
The type of the OMERO object |
| omero_port |
The port of the OMERO server |
| orcid |
The ORCID of the experimenter |
| output |
The output of the analysis |
| points |
A list of points included in the ROI |
| polygons |
A list of polygons included in the ROI |
| power_max_mw |
The maximum power measured in milliwatts |
| power_mean_mw |
The mean power measured in milliwatts |
| power_median_mw |
The median power measured in milliwatts |
| power_min_mw |
The minimum power measured in milliwatts |
| power_mw |
The power measured in milliwatts |
| power_samples |
This is a collection of power samples for different light sources |
| power_set_point |
The power set point as a fraction of the nominal power of the light source |
| power_std_mw |
The standard deviation of the power measured in milliwatts |
| preparation_protocol |
The protocol used to prepare a sample |
| processed |
Has the dataset been processed by microscope-metrics |
| processing_application |
The application used to process the dataset |
| processing_datetime |
The datetime of the processing by microscope-metrics |
| processing_entity |
The entity that processed the dataset |
| processing_log |
The log of the processing by microscope-metrics |
| processing_version |
The version of the application used to process the dataset |
| psf_beads_images |
The image containing the beads provided in the order TZYXC |
| r |
The red value of the color |
| rectangles |
A list of rectangles included in the ROI |
| roi_center_region |
Mask ROIs marking the area of maximum illumination |
| roi_centers_fitted |
Point ROIs marking the fitted center of the area of maximum illumination |
| roi_centers_geometric |
Point ROIs marking the geometric center of the area of maximum illumination |
| roi_centers_max_intensity |
Point ROIs marking the maximum intensity of the area of maximum illumination |
| roi_centers_of_mass |
Point ROIs marking the center of mass of the area of maximum illumination |
| roi_corners |
Rectangular ROIs used to compute the corner intensities |
| roi_profiles |
line ROIs used to compute the intensity profiles |
| sample |
The physical sample that was imaged |
| sampling_location |
The location at which the sampling was taken |
| saturation_threshold |
Tolerated saturation threshold |
| serial_number |
The serial number of a device |
| shape_c |
The shape of an image in the c dimension |
| shape_t |
The shape of an image in the t dimension |
| shape_x |
The shape of an image in the x dimension |
| shape_y |
The shape of an image in the y dimension |
| shape_z |
The shape of an image in the z dimension |
| sigma |
Input parameter: the sigma for the smoothing gaussian filter to be applied pr... |
| sigma_x |
Smoothing sigma to be applied to the image in the X axis |
| sigma_y |
Smoothing sigma to be applied to the image in the Y axis |
| sigma_z |
Smoothing sigma to be applied to the image in the Z axis |
| snr_threshold |
Signal to noise ratio threshold to be used for bead detection |
| source_images |
A list of references linking to the images that were used as a source |
| source_reference |
The source object of the column |
| source_roi |
The source ROI of the orthogonal image |
| stroke_color |
The stroke color of the shape |
| stroke_width |
The stroke width of the shape |
| t |
The t coordinate |
| table_data |
A non-required slot for non-serializable table data object |
| text |
The text of the comment |
| time_points_sec |
The relative times at which the time series were acquired in seconds |
| time_series |
A series representing time for time-lapse images |
| top_center_intensity_mean |
The mean intensity of the top-center of the image |
| top_center_intensity_ratio |
The mean intensity of the top-center of the image divided by the maximum int... |
| top_left_intensity_mean |
The mean intensity of the top-left corner of the image |
| top_left_intensity_ratio |
The mean intensity of the top-left corner of the image divided by the maximu... |
| top_right_intensity_mean |
The mean intensity of the top-right corner of the image |
| top_right_intensity_ratio |
The mean intensity of the top-right corner of the image divided by the maxim... |
| total_bead_count |
Total number of beads detected in the image |
| url |
The URL where the protocol can be found |
| validated |
Has the dataset been validated by a human |
| validation_datetime |
The datetime of the validation |
| values |
An optional container for the values of the column |
| version |
The version of the protocol |
| vertexes |
A list of vertexes defining the polygon |
| voxel_size_x_micron |
The physical size in the voxel in the x dimension in microns |
| voxel_size_y_micron |
The physical size in the voxel in the y dimension in microns |
| voxel_size_z_micron |
The physical size in the voxel in the z dimension in microns |
| w |
The width |
| warnings |
The warnings of the processing by microscope-metrics |
| wavelength_nm |
The wavelength of the light source in nanometers |
| x |
The x coordinate |
| x1 |
The x coordinate of the first point of the line |
| x2 |
The x coordinate of the second point of the line |
| y |
The y coordinate |
| y1 |
The y coordinate of the first point of the line |
| y2 |
The y coordinate of the second point of the line |
| z |
The z coordinate |