Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

Phillips, Michael A.; Pinto, David Miguel Susano; Hall, Nicholas; Mateos‐Langerak, Julio; Parton, Richard M.; Titlow, Josh; Stoychev, Danail; Parks, T.W.; Pinto, Tiago Susano; Sedat, John W.; Booth, Martin J.; Davis, Ilan; Dobbie, Ian M.

doi:10.1101/2021.01.18.427178

Cited by 5 publications

(5 citation statements)

References 34 publications

(49 reference statements)

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“…Other Python-based solutions for general control of optical microscopes exist ( Python Microscopy , Oxford Microscope-Cockpit 27 , Tormenta 28 , Storm-Control , MicroMator 29 ). Some of these software packages provide an out-of-the-box solution for standard acquisition modes ( e.g.…”

Section: Discussionmentioning

confidence: 99%

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Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging

Barho¹,

Fiche²,

Bardou³

et al. 2022

Open Res Europe

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Multiplexed sequential and combinatorial imaging enables the simultaneous detection of multiple biological molecules, e.g. proteins, DNA, or RNA, enabling single-cell spatial multi-omics measurements at sub-cellular resolution. Recently, we designed a multiplexed imaging approach (Hi-M) to study the spatial organization of chromatin in single cells. In order to enable Hi-M sequential imaging on custom microscope setups, we developed Qudi-HiM, a modular software package written in Python 3. Qudi-HiM contains modules to automate the robust acquisition of thousands of three-dimensional multicolor microscopy images, the handling of microfluidics devices, and the remote monitoring of ongoing acquisitions and real-time analysis. In addition, Qudi-HiM can be used as a stand-alone tool for other imaging modalities.

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Section: Discussionmentioning

confidence: 99%

“…Several software packages have been recently developed using Python for various imaging modalities. These include Qudi 26 , the software package Qudi-HiM is based on; Python Microscopy ; Oxford Microscope-Cockpit 27 ; Tormenta 28 ; Storm-Control ; and MicroMator 29 .…”

Section: Software Descriptionmentioning

confidence: 99%

Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging

Barho¹,

Fiche²,

Bardou³

et al. 2022

Open Res Europe

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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%

“…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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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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“…Microscope (Pinto et al, 2021) is a recent alternative for providing a resilient device layer in Python for controlling microscope devices. It is possible to script microscope experiments and use Cockpit (Phillips et al, 2021) as a GUI. However, the GUI is still limited to simpler microscopes.…”

Section: Architecture and Implementationmentioning

confidence: 99%