Friday, 26 Feb 2021

Semi-Automatic Analysis of Invasion and Migration Transwell Assays (I-AbACUS)

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Transwell assays are another common experimental approach for the quantification of migration and invasion (see also Automatic quantification of (cancer) cell invasiveness). This method relies on a semi-permeable membrane and a layer of Matrigel coating to simulate the extracellular matrix and thus represents a more realistic model of in-vivo migration. Its results, however, are highly dependent on the operator, as the number of migrated cells is often manually counted either from images acquired with an optical microscope, or directly from the instrument, with the help of a mechanical cell counter.
To address this limitation I-AbACUS was implemented. It couples a marker controlled watershed transform and an empirical filter to segment the cells and exclude membrane pores and debris from the count. A simple and intuitive graphical user interface allows for the interaction with the software and the correction of erroneously segmented regions.
Additionally the software integrates a machine learning procedure that allows for the improved segmentation of a specific cell type.

I Abacus

I-AbACUS is freely available both on this website and on as either matlab source code and compiled standalone application.

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Published in Computational Tools
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Marilisa Cortesi

Biomedical engineer graduated magna cum laude at the University of Bologna, Italy, in 2013. In 2017 she was awarded a PhD in Bioengineering from the same institution, with a thesis on computational modelling of complex biological processes and their application to the identification of potential therapeutic targets. More