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Organelle motility is essential for the correct cellular function of various eukaryotic cells. In plant cells, chloroplasts move towards the intracellular area irradiated by a weak light to maximise photosynthesis. To initiate this process, an unknown signal is transferred from the irradiated area to distant chloroplasts. Quantification of this chloroplast movement has been performed using visual estimations that are analyst-dependent and labour-intensive. Therefore, an objective and faster method is required.

In this study, we developed the cellssm package of R (https://github.com/hnishio/cellssm.git), which is a user-friendly tool for state-space modelling to statistically analyse the directional movement of cells or organelles. Our method showed a high accuracy in estimating the start time of chloroplast movement in the liverwort Marchantia polymorpha over a short period. The tool indicated that chloroplast …