Pycro-Manager: open-source software for customized and reproducible microscope control

Pinkard, Henry; Stuurman, Nico; Ivanov, Ivan E.; Anthony, Nicholas M.; Ouyang, Wei; Li, Bin; Yang, Bin; Tsuchida, Mark A.; Chhun, Bryant B.; Zhang, Grace; Mei, Ryan; Anderson, Michael; Shepherd, Douglas P.; Hunt-Isaak, Ian; Dunn, Raymond L.; Jahr, Wiebke; Kato, Saul; Royer, Loïc; Thiagarajah, Jay R.; Eliceiri, Kevin W.; Lundberg, Emma; Mehta, Shalin B.; Waller, Laura

doi:10.1038/s41592-021-01087-6

Cited by 62 publications

(55 citation statements)

References 9 publications

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“…We hope therefore that our program will be accessible for new users and democratize image analysis as well as forming a basis for advanced users to interrogate their data in depth. Particularly, there is enormous potential to integrate PySTACHIO into recent Python microscope control software [52], [53].…”

Section: Discussionmentioning

confidence: 99%

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PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data

Shepherd

Higgins

Wollman

et al. 2021

Preprint

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As camera pixel sensors grow larger and faster and optical microscopy techniques become ever more refined, there has been explosions in the quantity of data acquired during routine light microscopy. At the single-molecule level, this analysis involves multiple steps and can quickly become computationally expensive and intractable on ordinary office workstations. Moreover, complex bespoke software can present high activation barriers for new users. Here, we present our recent efforts to redevelop our quantitative single-molecule analysis routines into an optimized and extensible Python program, with both GUI and command-line implementations to facilitate its use on both local machines and remote clusters, and by beginners and advanced users alike. We demonstrate the performance of this code matches our previous MATLAB implementation but at a fraction of the computational cost. We show the code can extract fluorescence intensity values corresponding to single reporter dye molecules and, using these, to estimate molecular stoichiometries and single cell copy numbers of fluorescently labeled biomolecules. It can also evaluate diffusion coefficients for the relatively short single-particle tracking data that is characteristic of time-resolved image stacks. To facilitate benchmarking against other codes, we also include data simulation routines which may trivially be used to compare different analysis programs. Finally, we show that PySTACHIO works also with two-color data and can perform colocalization analysis based on overlap integrals, to infer interactions between differently labelled biomolecules. We hope that by making this freely available for use and modification we can make complex single-molecule analysis of light microscopy data more accessible.

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Section: Discussionmentioning

confidence: 99%

“…interrogate their data in depth. Particularly, there is enormous potential to integrate PySTACHIO into recent Python microscope control software [39], [40].…”

mentioning

confidence: 99%

PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data

Shepherd

Higgins

Wollman

et al. 2021

Preprint

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“…Python bindings were recently made available for MMCore, which is the device control layer of µManager, making it compatible with ImSwitch implementation (through the model device sub-layer). Pycro-Manager (Pinkard et al, 2021) provides access to µManager from Python and combines it with image processing and multiple applications. However, custom plugins must still be written for the µManager Java layer, making it complicated to use in complex devices without a pre-existing specialized implementation.…”

Section: Architecture and Implementationmentioning

confidence: 99%

ImSwitch: Generalizing microscope control in Python

Moreno¹,

Al-Kadhimi²,

Alvelid³

et al. 2021

JOSS

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“…Several dedicated software solutions have been developed for applications requiring real-time analysis, most notably efficient scanning of large and complex samples (eg Refs 2–5 ) and real-time control of cellular processes (eg Refs 6–12 ). However only a handful generic solutions have been proposed so far 13–16 . AutomatedFCS is a Fiji plugin that is part of the Microscopy Pipeline Constructor.…”

Section: Introductionmentioning

confidence: 99%

“…Very few generic tools have been developed so far to facilitate the realization of complex, reactive microscopy experiments. One notable exception is Pycro-Manager 14 . This powerful framework is built on top of µManager, a widely-used software 15,16 controlling a large range of microscopy hardware.…”

Section: Introductionmentioning

confidence: 99%

MicroMator: Open and Flexible Software for Reactive Microscopy

Fox

Fletcher

Fraisse

et al. 2021

Preprint

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Microscopy image analysis has recently made enormous progress both in terms of accuracy and speed thanks to machine learning methods. This greatly facilitates the online adaptation of microscopy experimental plans using real-time information of the observed systems and their environments. Here we report MicroMator, an open and flexible software for defining and driving reactive microscopy experiments, and present applications to single-cell control and single-cell differentiation.

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Pycro-Manager: open-source software for customized and reproducible microscope control

Cited by 62 publications

References 9 publications

PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data

PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data

ImSwitch: Generalizing microscope control in Python

MicroMator: Open and Flexible Software for Reactive Microscopy

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