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Open-Source Software


of the entire process. T e interoperability of SciScan with existing data pipelines is further enhanced by compatibility with the OME. T is allows any OME-capable soſt ware to load images recorded with SciScan along with any metadata without the need for proprietary import fi lters. T is makes SciScan the only open-source soſt ware package for LSM, which is free of charge, OME-compatible, and scriptable both internally and externally. T ese features reduce the time for initial setup and thereby increase research productivity. SciScan’s ability to interface with external soſt ware from within the programming environment used to process and analyze the data opens the door to numerous sophisticated and data-intensive applications, including closed-loop operation. T is makes experi- ments easily scalable, allowing a single user to fully automate data acquisition on multiple systems at the same time, enabling higher throughput data acquisition and allowing “big data” applications. More information about SciScan, including the download fi les, can be found on the SciScan Knowledge Base (sciscan.scientifi ca. uk.com).


Conclusion T is article describes a free, open-source, LabVIEW-based


Figure 5 : A single plane from a two-channel Z -stack of the Drosophila optical lobe labeled with GFP and red fl uorescent protein (RFP) taken in SciScan using a Scientifi ca Multiphoton Resonant System. Bar = 50 µm.


Discussion We presented here SciScan, a LabVIEW-based open-source


soſt ware package developed by Scientifi ca Ltd for the control of LSMs. Its primary application is to acquire imaging data with Scientifi ca’s multiphoton microscope range ( Figure 5 ). In addition, SciScan can be used for image acquisition with any LSM employing National Instruments DAQ hardware. T is includes most custom-built multiphoton microscopes and many commercial third-party systems. SciScan is provided free of charge to the scientifi c community and operates standard galvanometer scanners as well as resonant scanners. SciScan allows researchers to control image acquisition from pre-prepared scripts via SciScript or externally via its ActiveX API. T is enables scientists to integrate SciScan into the same environments used for post-processing and data analysis. T us, SciScan directly connects the data acquisition process with the data pipeline or workfl ow, facilitating automation


soſt ware framework for controlling two-photon laser scanning experiments on any LSM. It is compatible with the OME, allowing any OME-capable soſt ware to load images recorded with SciScan along with any metadata without the need for proprietary import fi lters. It is also scriptable both internally and externally, allowing image registration over long-term experiments.


References [1] W Denk et al ., Science 248 ( 1990 ) 73 –7 6 . [2] F Helmchen and W Denk , Nat Methods 2 ( 2005 ) 932 – 40 . [3] K Ohki et al ., Nature 433 ( 2005 ) 597 – 603 . [4] DA Dombeck et al ., Neuron 56 ( 2007 ) 43 – 57 . [5] JN Stirman et al ., Nat Biotechnol 34 ( 2016 ) 857 – 62 . [6] KR Chi , Nat Methods 5 ( 2008 ) 651 – 58 . [7] TA Pologruto et al ., Biomed Eng Online 2 ( 2003 ) 13 . [8] Q-T Nguyen et al ., J Neurosci Methods 156 ( 2006 ) 351 – 59 . [9] D Langer et al ., J Neurosci Methods 215 ( 1 ) (2013 ) 38 – 52 . [10] L Campagnola et al ., Front Neuroinformatics 8 ( 2014 ) 3 . [11] IG Goldberg et al ., Genome Biol 6 ( 2005 ) R47 . [12] WS Rasband , ImageJ. , U.S. National Institutes of Health , Bethesda, MD , 1997 .


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