The revolution in light sheet microscopy enables the concurrent observation of thou-sands of dynamic processes, from single molecules to cellular organelles, with high spatiotemporal reso-lution. However, challenges in the interpretation of multidimensional data requires the fully automaticmeasurement of those motions to link local processes to cellular functions. This includes the design andthe implementation of image processing pipelines able to deal with diverse motion types, and 3D visual-ization tools adapted to the human visual system.

we developped a new method for 3D motion estimation that addresses the aforementionedissues. We integrate 3D matching and variational approach to handle a diverse range of motion withoutany prior on the shape of moving objects. We compare different similarity measures to cope with intensity ambiguities and demonstrate the effectiveness of the Census signature for both stages. Additionally, wepresent two intuitive visualization approaches to adapt complex 3D measures into an interpretable 2Dview, and a novel way to assess the quality of flow estimates in absence of ground truth.

Try Flowscope

Flow caclulation
Flowscope is available on the Allgo platform (you need an account)
Flowscope gives three images named *soru.tif, *sorv.tif and *sorw.tif. These three images correspond to the flow coordinates in the 3 directions of space.

Flow visualisation
To visualize the calculated flow a tool is available on the Allgo platform (you need an account)


S. Manandhar, P. Bouthemy, E. Welf, G. Danuser, P. Roudot, C. Kervrann. 3D flow field estimation and assessment for live cell fluorescence microscopy. Bioinformatics, pp. 1-19, btz780, HAL-INRIA-02308001, 2019

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