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

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

doi:10.1038/s41592-021-01087-6

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

Nat Methods. 2021 Mar;18(3):226-228. doi: 10.1038/s41592-021-01087-6.

Authors

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. [email protected].
² Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA, USA. [email protected].
³ Berkeley Institute for Data Science, University of California, Berkeley, Berkeley, CA, USA. [email protected].
⁴ University of California San Francisco Bakar Computational Health Sciences Institute, San Francisco, CA, USA. [email protected].
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.

No abstract available

Publication types

Letter
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Data Collection / instrumentation
Data Collection / methods
Microscopy / instrumentation
Microscopy / methods*
Programming Languages
Software*

Publication types

MeSH terms

Grants and funding