Abstract: This paper describes a clustering-based music transcription method that estimates the piano rolls of arbitrary musical instrument parts from multi-instrument polyphonic music signals. If target musical pieces are always played by particular kinds of musical instruments, a way to obtain piano rolls is to compute the pitchgram (pitch saliency spectrogram) of each musical instrument by using a deep neural network (DNN). However, this approach has a critical limitation that it has no way to deal with musical pieces including undefined musical instruments. To overcome this limitation, we estimate a condensed pitchgram with an existing instrument-independent neural multi-pitch estimator and then separate the pitchgram into a specified number of musical instrument parts with a deep spherical clustering technique. To improve the performance of transcription, we propose a joint spectrogram and pitchgram clustering method based on the timbral and pitch characteristics of musical instruments. The experimental results show that the proposed method can transcribe musical pieces including unknown musical instruments as well as those containing only predefined instruments, at the state-of-the-art transcription accuracy.