Description of the tracker output¶
The segmentation as well as optionally quantified fluorescent signal data can be accessed anytime and is stored in the SegmentationData and QuantificationData class of Tracx. See data_access for details how to work with the data object.
To save the full Tracx results run:
Tracker.saveTrackerResultsAsTable()
This will save the Tracx results as a table (also accessible under Tracker.data.joinedTrackerDataTable or Tracker.data.joinedTrackerData). Each row contains the data of a segmented cell for a given image/frame. The column headers are described below in the table along with the units or symbols used in the publication.
Data field name |
Unit |
Symbol |
Description |
|---|---|---|---|
cell_frame |
\(t\) |
The frame number |
|
cell_index |
\(s(t)\) |
The segmentation index of the cell in this frame of the labeled segmentation mask |
|
cell_center_x |
\(s_x\) |
x coordinate of the cell center |
|
cell_center_y |
\(s_y\) |
y coordinate of the cell center |
|
cell_center_z |
\(s_z\) |
z coordinate of the cell center |
|
cell_majoraxis |
px |
Length of the cell major axis |
|
cell_minoraxis |
px |
Length of the cell minor axis |
|
cell_orientation |
deg |
Angle between the image x axis and the cell major axis |
|
cell_area |
px |
Total cell area |
|
cell_volume |
voxels |
Total cell volume |
|
cell_perimeter |
px |
Cell perimeter |
|
cell_eccentricity |
Cell eccentricity |
||
cell_fractionOfGoodMembranePixels |
Fraction if good membrane pixels |
||
cell_mem_area |
px |
Cell membrane area |
|
cell_mem_volume |
voxels |
Cell membrane volume |
|
cell_nuc_radius |
Radius of the nucleus |
||
cell_nuc_area |
px |
Nucleus area |
|
cell_dif_x |
px |
x coordinate movement of the cell center in respect to the previous frame |
|
cell_dif_y |
px |
y coordinate movement of the cell center in respect to the previous frame |
|
cell_dif_z |
px |
z coordinate movement of the cell center in respect to the previous frame |
|
cell_filtered_dif_x |
px |
Gaussian filtered x coordinate movement of the cell center in respect to the previous frame |
|
cell_filtered_dif_y |
px |
Gaussian filtered y coordinate movement of the cell center in respect to the previous frame |
|
cell_filtered_dif_z |
px |
Gaussian filtered z coordinate movement of the cell center in respect to the previous frame |
|
cell_pole1_x |
\(Po_1\) |
x coordinate of the cell pole 1; symmetrical division lineage information |
|
cell_pole1_y |
\(Po_1\) |
y coordinate of the cell pole 1; symmetrical division lineage information |
|
cell_pole2_x |
\(Po_2\) |
x coordinate of the cell pole 2; symmetrical division lineage information |
|
cell_pole2_y |
\(Po_2\) |
x coordinate of the cell pole 2; symmetrical division lineage information |
|
cell_pole1_age |
Cell pole 1 replicative age; symmetrical division lineage information. Nan for cells on first frame then increasing by 1 with every division |
||
cell_pole2_age |
Cell pole 2 replicative age; symmetrical division lineage information. Nan for cells on first frame then increasing by 1 with every division |
||
cell_timepoint |
\(t\) |
The frame number (internal) |
|
cell_zplane |
The z plane number |
||
track_index |
The track index |
||
track_index_qc |
The track index; used internally |
||
track_fingerprint_real_distance |
\(d_f\) |
The real cell region fingerprint |
|
track_age |
The track age; used internally to count the frames where the segmentation is missing depends on the ‘maxFrameSkipping’ parameter |
||
track_parent |
The parent track to the current track |
||
track_parent_frame |
The parent track frame |
||
track_parent_prob |
The probability of the parent track assignment |
||
track_parent_score |
Score for the parent track assignment |
||
track_generation |
Generation number of the track |
||
track_lineage_tree |
The unique identifier for the cell lineage |
||
track_cell_cycle_phase |
The cell cycle phase of the track; G1 (1) and S/G2/M (2) |
||
track_assignment_fraction |
\(F_f\) |
The neighbourhood based assignment fraction |
|
track_total_assignment_cost |
\(C\) |
The final total assignment cost of the LAP; depends on ‘usedFunctionsForCostMatrix’ and ‘individualFunctionPenalty’ parameter |
|
track_position_assignment_cost |
\(C^{disp}\) |
The final position assignment cost of the LAP; depends on ‘usedFunctionsForCostMatrix’ and ‘individualFunctionPenalty’ parameter |
|
track_area_assignment_cost |
\(C^{size}\) |
The final area assignment cost of the LAP; depends on ‘usedFunctionsForCostMatrix’ and ‘individualFunctionPenalty’ parameter |
|
track_rotation_assignment_cost |
\(C^{rot}\) |
The final rotation assignment cost of the LAP; depends on ‘usedFunctionsForCostMatrix’ and ‘individualFunctionPenalty’ parameter |
|
track_frame_skipping_cost |
\(C^{skip}\) |
The final frame skipping cost of the LAP; depends on ‘usedFunctionsForCostMatrix’ and ‘individualFunctionPenalty’ parameter |
|
track_start_frame |
The start frame of the track |
||
track_end_frame |
The end frame of the track |
||
track_index_corrected |
The track index corrected after manual correction |
||
track_contained_in_track |
The track index of another track; If a track is part of another longer track i.e due to mis-segmentation |
||
track_has_bud |
If the cell of the track on the current frame is budding (asymetrical division, yeast only) |
||
track_budneck_total |
Budneck total marker signal (asymetrical division, yeast only) |
||
cell_mask_boundary_points |
Boundary points of the cell (internal) |
||
fluo_id |
Numeric fluorescence channel identifier i.e. 1, 2 |
||
fluo_name |
Name of the fluorecence channel identifier i.e. GFP, YFP |
||
fluo_background_mean |
Mean value of the image background |
||
fluo_background_std |
Standard deviation of the image background |
||
fluo_cell_total |
Total membrane fluorescence |
||
fluo_cell_q75 |
75th percentile of membrane fluorescence distribution |
||
fluo_cell_q50 |
Median of membrane fluorescence distribution |
||
fluo_cell_q25 |
25th percentile of membrane fluorescence distribution |
||
fluo_mem_total |
Total membrane fluorescence |
||
fluo_mem_q75 |
75th percentile of membrane fluorescence distribution |
||
fluo_mem_q50 |
Median of membrane fluorescence distribution |
||
fluo_mem_q25 |
25th percentile of membrane fluorescence distribution |
||
fluo_nuc_total |
Total nucleus fluorescence. The nucleus area is defined as the set of pixels that form the brightest disk in the cell interior. The radius of that disk is automatically adjusted based on the value X that denotes the nuclear volume fraction in the cell. X can be adjusted by the user in the advanced parameters (default value is 0.07). |
||
fluo_nuc_q75 |
75th percentile of nucleus fluorescence distribution |
||
fluo_nuc_q50 |
median of nucleus fluorescence distribution |
||
fluo_nuc_q25 |
25th percentile of nucleus fluorescence distribution |
||
fluo_bright_total |
Total fluorescence of the cell’s bright area. The cell’s bright area is defined as the set of (100*X)% brightest pixels found in the cell. X can be adjusted by the user in the advanced parameters (default value is 0.3). |
||
fluo_bright_q75 |
75th percentile of the cell’s bright area fluorescence distribution |
||
fluo_bright_q50 |
median of the cell’s bright area fluorescence distribution |
||
fluo_bright_q25 |
25th percentile of the cell’s bright area fluorescence distribution |
||
fluo_bright_euler |
Euler number of the cell’s bright area |
More information about the basic segmentation and quantification data can be found in the original CellX publication (CellX).
Additional Tracx outputs are:
Control images with the prefix tracked_control* returns an image for each frame where all cells are labeled with the track index
Control images with the prefix tracked_control_mask* returns an image for each frame where all tracks are colored by a unique color
Relabeled segmentation masks with the track indices track_mask*