Logging

Currently we support monitoring the training progress in Tensorboard while basic metrics are reported to the console as well. All metrics that include comparison to ground truth emitters are based on the parameters (implicitly) provided in the configuration .yaml file. Those include match dimensionality (i.e., in 2D or 3D) and max. allowed distances. The threshold on the detection filters the detections prior to matching.

Tensorboard

Metrics

Abbreviation	Name	Description
prec	Precision	Number of true positives over all detections
rec	Recall	Number of true positives over all (ground truth) localizations
jac	Jaccard	Intersection over Union
f1	F1 Score	2 x Precision x Recall over (Precision + Recall)
effcy_lat	Efficiency lateral	SMLM Challenge defined efficiency lateral
effcy_ax	Efficiency axial	SMLM Challenge defined efficiency axial
effcy_vol	Efficiency volumetric	SMLM Challenge defined efficiency volumetric
rmse_lat	RMSE lateral	Root Mean Square Error lateral
rmse_ax	RMSE axial	Root Mean Square Error axial (z)
rmse_vol	RMSE volumetric	Root Mean Square Error volumetric
mad_lat	MAD lateral	Mean Absolute Deviation lateral
mad_ax	MAD axial	Mean Absolute Deviation axial
mad_vol	MAD volumetric	Mean Absolute Deviation volumetric

Other (non or less-semantic) metrics

Abbreviation	Description
learning_rate	Learning Rate
test_ep	Test loss per epoch
train_batch	Train loss per batch
train_ep	Train loss per epoch
loss_cmp_0	Gaussian localization loss
loss_cmp_1	Background loss

Distributions

Abbreviation	Description
dist/prob	Probability distribution of active pixels (active typically means above p >= 0.6)
dist/x_offset	Distribution of relative offset to pixel border in x direction
dist/y_offset	Distribution of relative offset to pixel border in y direction
residuals/phot_gt_pred	Predicted vs ground truth photon counts
residuals/z_gt_pred	Predicted vs ground truth z values

In- Output Logging

Input shows a sampled input frame with ground truth emitters. Output shows the respective output channels of the model.

Emitter-Out and Emitter-Match

Abbreviation	Description
em_match	All matched emitter pairs
em_match_3d	All matched emitter pairs in 3D
em_out	All ground truth emitters and all predicted emitters
em_out_3d	All ground truth emitters and all predicted emitters in 3D