| acquisition_date |
The date of the acquisition |
| alpha |
The alpha value of the color (optional) |
| argolight_b_image |
Input parameter: image of the argolight b pattern provided as a 5D numpy arra... |
| argolight_e_image |
Image of the argolight e pattern provided as a 5D numpy array in the order TZ... |
| authors |
The authors of the protocol |
| axis |
Axis along which resolution is being measured |
| b |
The blue value of the color |
| 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 |
|
| center_of_illumination |
Point ROIs marking the center of illumination |
| center_of_mass_x |
The x coordinate of the center of mass of the center of illumination region |
| center_of_mass_y |
The y coordinate of the center of mass of the center of illumination region |
| center_threshold |
Input parameter: relative threshold for what is going to be considered as the... |
| channel |
The channel number to which the measurements apply |
| channel_A |
The first channel number to which the measurements apply |
| channel_B |
The second channel number to which the measurements apply |
| columns |
A list of the columns of the table |
| comment |
A human readable comment about the dataset |
| corner_fraction |
Input parameter: the proportion of the image to be considered as corner or ce... |
| corner_rois |
ROIs used to compute the corner intensities |
| data |
|
| decile_0 |
The 0th decile of the intensity distribution of the maximum intensity |
| decile_1 |
The 1st decile of the intensity distribution of the maximum intensity |
| decile_2 |
The 2nd decile of the intensity distribution of the maximum intensity |
| decile_3 |
The 3rd decile of the intensity distribution of the maximum intensity |
| decile_4 |
The 4th decile of the intensity distribution of the maximum intensity |
| decile_5 |
The 5th decile of the intensity distribution of the maximum intensity |
| decile_6 |
The 6th decile of the intensity distribution of the maximum intensity |
| decile_7 |
The 7th decile of the intensity distribution of the maximum intensity |
| decile_8 |
The 8th decile of the intensity distribution of the maximum intensity |
| decile_9 |
The 9th decile of the intensity distribution of the maximum intensity |
| description |
A description of an entity |
| df |
A Pandas DataFrame object |
| distance_measurements |
Key Distance Measurements on Argolight spots |
| experimenter |
The experimenter that performed the imaging experiment |
| field_illumination_image |
Input parameter: homogeneity image provided as a numpy array in the order |
| fill_color |
The fill color of the shape |
| focus_slice |
Z position at which focus has been measured |
| g |
The green value of the color |
| h |
The height of the rectangle |
| id |
The unique identifier for an entity |
| image |
The image to which the ROI is applied |
| image_url |
An URL linking to the image |
| input |
An input element for the analysis |
| intensity_map |
Intensity map of the field illumination |
| intensity_map_size |
Input parameter: the size of the output intensity map in pixels |
| intensity_max_spot |
Integrated intensity of the most intense spot for each channel |
| intensity_max_spot_roi |
ROI number of the most intense spot for each channel |
| intensity_measurements |
Key Intensity Measurements on Argolight spots |
| intensity_min_spot |
Integrated intensity of the least intense spot for each channel |
| intensity_min_spot_roi |
ROI number of the least intense spot for each channel |
| intensity_profiles |
Intensity profiles of the argolight lines provided as tables |
| is_open |
Is the polygon open |
| key_measurements |
Key Measurements on Argolight E images |
| key_values |
Key-Value pairs containing the Key measurements for the field illumination an... |
| label |
The label of the ROI |
| lower_threshold_correction_factors |
Input parameter: correction factor for the lower thresholds |
| mad_3d_dist |
Median absolute deviation of the 3D distances between spots for each permutat... |
| mad_mean_intensity |
Median absolute deviation of all spots integrated intensity for each channel |
| mad_z_dist |
Median absolute deviation of the Z distances between spots for each permutati... |
| mask |
The mask image |
| max_intensity |
The maximum intensity of the center of illumination |
| max_intensity_pos_x |
The x coordinate of the maximum intensity of the center of illumination |
| max_intensity_pos_y |
The y coordinate of the maximum intensity of the center of illumination |
| mean_3d_dist |
Mean of the 3D distances between spots for each permutation of channel A and ... |
| mean_intensity |
Mean of all spots integrated intensity for each channel |
| mean_z_dist |
Mean of the Z distances between spots for each permutation of channel A and B |
| measured_band |
Fraction of the image across which intensity profiles are measured |
| median_3d_dist |
Median of the 3D distances between spots for each permutation of channel A an... |
| median_intensity |
Median of all spots integrated intensity for each channel |
| median_z_dist |
Median of the Z distances between spots for each permutation of channel A and... |
| 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_max_intensity_ratio |
Ratio between the integrated intensities between the most intense and the lea... |
| name |
The name of an entity |
| nb_pixels |
The area occupied by the center of illumination region |
| nr_of_spots |
Number of argolight spots detected for each channel |
| orcid |
The ORCID of the experimenter |
| output |
An output element from the analysis |
| peak_height_A |
Height of first peak in the intensity profiles |
| peak_height_B |
Height of second peak in the intensity profiles |
| peak_position_A |
Position of first peak in the intensity profiles |
| peak_position_B |
Position of second peak in the intensity profiles |
| peak_prominence_A |
Prominence of first peak in the intensity profiles |
| peak_prominence_B |
Prominence of second peak in the intensity profiles |
| peaks_rois |
ROIs of the peaks found in the argolight images |
| processed |
Has the dataset been processed by microscope-metrics |
| processing_date |
The date of the processing by microscope-metrics |
| processing_log |
The log of the processing by microscope-metrics |
| profile_rois |
ROIs used to compute the intensity profiles |
| prominence_threshold |
Peak prominence used as a threshold to distinguish two peaks |
| protocol |
The protocol used to prepare the sample |
| r |
The red value of the color |
| rayleigh_resolution |
Rayleigh resolution measured |
| remove_center_cross |
Input parameter: remove the center cross found in some Argolight patterns |
| sample |
The sample that was imaged |
| saturation_threshold |
Tolerated saturation threshold |
| shapes |
|
| sigma |
Input parameter: the sigma for the smoothing gaussian filter to be applied pr... |
| sigma_x |
Input parameter: smoothing factor for objects detection in the X axis |
| sigma_y |
Input parameter: smoothing factor for objects detection in the Y axis |
| sigma_z |
Input parameter: smoothing factor for objects detection in the Z axis |
| source_image_url |
A list of URLs linking to the images that were used as a source |
| spots_centroids |
Centroids of the argolight spots provided as a list of ROIs, one per channel |
| spots_distance |
Input parameter: distance between argolight spots |
| spots_distances |
Table of distances between argolight spots |
| spots_labels_image |
Labels image of the argolight segmented spots provided as a 5D numpy array in... |
| spots_properties |
Table of properties of the argolight spots |
| std_3d_dist |
Standard deviation of the 3D distances between spots for each permutation of ... |
| std_mean_intensity |
Standard deviation of all spots integrated intensity for each channel |
| std_z_dist |
Standard deviation of the Z distances between spots for each permutation of c... |
| stroke_color |
The stroke color of the shape |
| stroke_width |
The stroke width of the shape |
| t |
|
| text |
The text of the tag |
| 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... |
| type |
The type of the sample |
| upper_threshold_correction_factors |
Input parameter: correction factor for the upper thresholds |
| url |
The URL where the protocol can be found |
| values |
|
| version |
The version of the protocol |
| vertexes |
A list of vertexes defining the polygon |
| w |
The width of the rectangle |
| x |
|
| x1 |
The x coordinate of the first point of the line |
| x2 |
The x coordinate of the second point of the line |
| x_rad |
The x radius of the ellipse |
| y |
|
| y1 |
The y coordinate of the first point of the line |
| y2 |
The y coordinate of the second point of the line |
| y_rad |
The y radius of the ellipse |
| z |
|