Baleen whales produce a wide variety of frequency-modulated calls. Extraction of the time-frequency (TF) structures of these calls forms the basis for many applications, including abundance estimation and species recognition. Typical methods to extract the contours of whale calls from a spectrogram are based on the short-time Fourier transform and are, thus, restricted by a fixed TF resolution. Considering the low-frequency nature of baleen whale calls, this work represents the contours using a pseudo-Wigner-Ville distribution for a higher TF resolution at the cost of introducing cross terms. An adaptive threshold is proposed followed by a modified Gaussian mixture probability hypothesis density filter to extract the contours. Finally, the artificial contours, which are caused by the cross terms, can be removed in post-processing. Simulations were conducted to explore how the signal-to-noise ratio influences the performance of the proposed method. Then, in experiments based on real data, the contours of the calls of three kinds of baleen whales were extracted in a highly accurate manner (with mean deviations of 5.4 and 0.051 Hz from the ground-truth contours at sampling rates of 4000 and 100 Hz, respectively) with a recall of 75% and a precision of 78.5%.