Learning with minimal effort: leveraging in silico labeling for cell and nucleus segmentationThomas Bonte, Maxence Philbert, Emeline Coleno et al.
Deep learning provides us with powerful methods to perform nucleus or cell segmentation with unprecedented quality. However, these methods usually require large training sets of manually annotated images, which are tedious and expensive to generate. In this paper we propose to use In Silico Labeling (ISL) as a pretraining scheme for segmentation tasks. The strategy is to acquire label-free microscopy images (such as bright-field or phase contrast) along fluorescently labeled images (such as DAPI or CellMask). We then train a model to predict the fluorescently labeled images from the label-free microscopy images. By comparing segmentation performance across several training set sizes, we show that such a scheme can dramatically reduce the number of required annotations.
ml_edm package: a Python toolkit for Machine Learning based Early Decision MakingAurélien Renault, Youssef Achenchabe, Édouard Bertrand et al.
\texttt{ml\_edm} is a Python 3 library, designed for early decision making of any learning tasks involving temporal/sequential data. The package is also modular, providing researchers an easy way to implement their own triggering strategy for classification, regression or any machine learning task. As of now, many Early Classification of Time Series (ECTS) state-of-the-art algorithms, are efficiently implemented in the library leveraging parallel computation. The syntax follows the one introduce in \texttt{scikit-learn}, making estimators and pipelines compatible with \texttt{ml\_edm}. This software is distributed over the BSD-3-Clause license, source code can be found at \url{https://github.com/ML-EDM/ml_edm}.