Publication

Reproducible image-based profiling with Pycytominer

2025

Abstract

Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Next, whether by deep learning or classical algorithms, image analysis pipelines commonly produce single-cell features. To process these single cells for downstream applications, we present Pycytominer, a user-friendly, open-source Python package that implements the bioinformatics steps key to image-based profiling. We demonstrate Pycytominer’s usefulness in a machine-learning project to predict nuisance compounds that cause undesirable cell injuries.

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2025

Abstract

Official source

Related concepts (32)

Quantum algorithm

In quantum computing, a quantum algorithm is an algorithm which runs on a realistic model of quantum computation, the most commonly used model being the quantum circuit model of computation. A classical (or non-quantum) algorithm is a finite sequence of instructions, or a step-by-step procedure for solving a problem, where each step or instruction can be performed on a classical computer. Similarly, a quantum algorithm is a step-by-step procedure, where each of the steps can be performed on a quantum computer.

Shor's algorithm

Shor's algorithm is a quantum algorithm for finding the prime factors of an integer. It was developed in 1994 by the American mathematician Peter Shor. It is one of the few known quantum algorithms with compelling potential applications and strong evidence of superpolynomial speedup compared to best known classical (that is, non-quantum) algorithms. On the other hand, factoring numbers of practical significance requires far more qubits than available in the near future.

Quantum algorithm for linear systems of equations

The quantum algorithm for linear systems of equations, also called HHL algorithm, designed by Aram Harrow, Avinatan Hassidim, and Seth Lloyd, is a quantum algorithm published in 2008 for solving linear systems. The algorithm estimates the result of a scalar measurement on the solution vector to a given linear system of equations. The algorithm is one of the main fundamental algorithms expected to provide a speedup over their classical counterparts, along with Shor's factoring algorithm, Grover's search algorithm, and the quantum fourier transform.

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Reproducible image-based profiling with Pycytominer

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