Cell Shape Dynamics

Application

Cell Shape Dynamics Analysis Using ilastik, Fiji and AmoePy. 

Problem & Motivation

Accurate cell contour extraction is a prerequisite for reliable cell shape dynamics analysis. The workflow combines pixel classification in ilastik, mask refinement in Fiji, and quantitative shape analysis in AmoePy to generate kymographs and spatiotemporal measurements of cell morphology.

Outputs

The final outputs include:

• • High-quality cell masks generated by ilastik and Fiji
  • Standardized contour coordinate files
  • Quantitative measurements of spatiotemporal cell shape dynamics in AmoePy

Esteban, A. M., et al., Reproducibility Assessment of Cell Shape Transition Analysis in AmoePy. XXXXX, XXXXXX.

Moldenhawer, T., et al., Spontaneous transitions between amoeboid and keratocyte-like modes of migration. Front Cell Dev Biol, 2022. 10: p. 898351.

Schindler, D., et al., Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows. PLoS Comput Biol, 2021. 17(8): p. e1009268.

Moldenhawer, T., et al., A Hands-on Guide to AmoePy – a Python-Based Software Package to Analyze Cell Migration Data. Methods Mol Biol, 2024. 2828: p. 159-184.

Daniel Schindler, T.M., Lena Lindenmeier, Victor Lesur, Matthias Holschneider, AmoePy. 2025.

Schindelin, J., et al., The ImageJ ecosystem: An open platform for biomedical image analysis. Mol Reprod Dev, 2015. 82(7-8): p. 518-29.

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Berg, S., et al., ilastik: interactive machine learning for (bio)image analysis. Nat Methods, 2019. 16(12): p. 1226-1232.