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

Henry Pinkard^{1

2

3

4}, Nico Stuurman⁵, Ivan E Ivanov⁶, Nicholas M Anthony⁷, Wei Ouyang⁸, Bin Li⁹, Bin Yang⁶, Mark A Tsuchida⁹, Bryant Chhun⁶, Grace Zhang¹⁰, Ryan Mei¹⁰, Michael Anderson^{11

12}, Douglas P Shepherd¹³, Ian Hunt-Isaak¹⁴, Raymond L Dunn¹⁵, Wiebke Jahr¹⁶, Saul Kato^{17

18

19}, Loïc A Royer⁶, Jay R Thiagarajah^{11

12}, Kevin W Eliceiri⁹, Emma Lundberg⁸, Shalin B Mehta⁶, Laura Waller^{10

20}

Affiliations

¹ Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA. hbp@berkeley.edu.
² Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA, USA. hbp@berkeley.edu.
³ Berkeley Institute for Data Science, University of California, Berkeley, Berkeley, CA, USA. hbp@berkeley.edu.
⁴ University of California San Francisco Bakar Computational Health Sciences Institute, San Francisco, CA, USA. hbp@berkeley.edu.
⁵ Howard Hughes Medical Institute and University of California, San Francisco, San Francisco, CA, USA.
⁶ Chan Zuckerberg Biohub, San Francisco, CA, USA.
⁷ Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
⁸ Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.
⁹ University of Wisconsin at Madison, Madison, WI, USA.
¹⁰ Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.
¹¹ Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
¹² Harvard Medical School, Boston, MA, USA.
¹³ Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ, USA.
¹⁴ Applied Physics Graduate Program, John Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
¹⁵ Neuroscience Graduate Program, Department of Neurology, Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA.
¹⁶ Institute of Science and Technology Austria, Klosterneuburg, Austria.
¹⁷ Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
¹⁸ Weill Institute for Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
¹⁹ Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
²⁰ Berkeley Institute for Data Science, University of California, Berkeley, Berkeley, CA, USA.

PMID: 33674797
PMCID: PMC8532176
DOI: 10.1038/s41592-021-01087-6

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

Henry Pinkard et al. Nat Methods. 2021 Mar.

. 2021 Mar;18(3):226-228.

doi: 10.1038/s41592-021-01087-6.

Authors

Affiliations

¹ Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA. hbp@berkeley.edu.
² Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA, USA. hbp@berkeley.edu.
³ Berkeley Institute for Data Science, University of California, Berkeley, Berkeley, CA, USA. hbp@berkeley.edu.
⁴ University of California San Francisco Bakar Computational Health Sciences Institute, San Francisco, CA, USA. hbp@berkeley.edu.
⁵ Howard Hughes Medical Institute and University of California, San Francisco, San Francisco, CA, USA.
⁶ Chan Zuckerberg Biohub, San Francisco, CA, USA.
⁷ Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
⁸ Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.
⁹ University of Wisconsin at Madison, Madison, WI, USA.
¹⁰ Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.
¹¹ Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
¹² Harvard Medical School, Boston, MA, USA.
¹³ Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ, USA.
¹⁴ Applied Physics Graduate Program, John Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
¹⁵ Neuroscience Graduate Program, Department of Neurology, Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA.
¹⁶ Institute of Science and Technology Austria, Klosterneuburg, Austria.
¹⁷ Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
¹⁸ Weill Institute for Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
¹⁹ Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
²⁰ Berkeley Institute for Data Science, University of California, Berkeley, Berkeley, CA, USA.

PMID: 33674797
PMCID: PMC8532176
DOI: 10.1038/s41592-021-01087-6

No abstract available

PubMed Disclaimer

Conflict of interest statement

Competing Interests The authors declare no competing interests.

Figures

**Figure 1:**
**a) Software architecture overview.** (Grey) The existing parts of μManager provide generic microscope control abstracted from specific hardware, a graphical user interface (GUI), a Java plugin interface, and an acquisition engine, which automates various aspects of data collection. (Orange) Pycro-Manager enables access to these components through Python over a network-compatible transport layer, as well as a concise, high-level programming interface for acquiring data. These provide integration of data acquisition with (purple) Python libraries for hardware control, data visualization, scientific computing, etc. **b) Pycro-Manager’s high-level programming interface.** The data acquisition process in Pycro-Manager starts with (blue) a source of acquisition events (from either a programming or GUI). These events are passed to (green) the acquisition engine, which optimizes them to take advantage of hardware triggering where available, sends instructions to hardware, and acquires images. (M⁴agenta) The resulting images are then saved and displayed in the GUI. The three main abstractions of the Pycro-Manager high-level programming interface (acquisition events, acquisition hooks, and image processors) enable fine-grained control and customization of this process. c) **Code examples.** Code snippets for implementing (blue) acquisition events, (green) acquisition hooks, and (magenta) image processors.

See this image and copyright information in PMC

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

Affiliations

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

Authors

Affiliations

Conflict of interest statement

Figures

References

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MeSH terms

Grants and funding

LinkOut - more resources

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