This page contains a Flash digital edition of a book.
Open-Source Software for Controlling Two-Photon Laser Scanning Microscopes


George Ward ,* Alex Murray , and Christian Wilms Scientifi ca , Uckfi eld , TN22 1QQ , United Kingdom


* george.ward@scientifi ca.uk.com


Abstract: T wo-photon laser scanning microscopy is widely used in the biological sciences largely because of its ability to resolve structures deep within highly scattering tissue. Various proprietary or open-source software packages are available for controlling laser scanning microscopes. However, integration with third-party or custom-built hardware and software can be challenging. Here, we present SciScan, a free, open-source, LabVIEW-based software framework for controlling two-photon laser scanning experiments with exceptional flexibility, including an application programming interface (API) for automating experimental workflow.


Introduction


Over the past 25 years two-photon laser scanning microscopy (LSM) has revolutionized research in neuroscience, immunology, and many other fi elds because it enables scientists to investigate the structure and function of intact tissue in living animals at diff raction- limited resolution [ 1 , 2 ]. For example, neuroscientists routinely use two-photon microscopy to monitor brain activity in awake animals with sub-cellular resolution while the animal performs behavioral tasks or responds to sensory stimulation [ 3 – 5 ].


Typically, researchers integrate additional equipment (for


example, XY stages, instruments for sensory or optogenetic stimulation, electrophysiology amplifi ers) with their two-photon microscope to accommodate a set of experiments. T is oſt en


involves custom-built hardware controlled by custom-written soſt ware. Commercially available two-photon microscopes usually include proprietary control soſt ware that allows users to operate the microscope and acquire images. However, customizing this basic functionality to interface with custom hardware and soſt ware or to automate complex experimental procedures can be a challenge, as manufacturers are oſt en reluctant to disclose their designs. Several soſt ware packages for operating two-photon laser scanning microscopes (LSMs) are commercially [ 6 ] or freely [ 7 – 10 ] available in various programming languages including C++, LabVIEW, MATLAB, and Python. However, none of these soſt ware packages enables the end user to easily interface with any arbitrary programming language they may already be familiar with. T is is a substantial drawback for scientists who intend to integrate a commercial or custom-built two-photon LSM within an existing soſt ware framework. T is article describes SciScan: a free, open-source soſt ware package with an ActiveX-based application programming interface (API) for external scripting. All commonly used data analysis and programming environments such as MATLAB, Python, C++, or Java off er ActiveX support, thereby enabling the researcher to integrate SciScan within the same environments they already use


Figure 1 : GUI of SciScan’s main display window including the main controls and the image display. 12 doi: 10.1017/S1551929517000785 www.microscopy-today.com • 2017 September


Page 1  |  Page 2  |  Page 3  |  Page 4  |  Page 5  |  Page 6  |  Page 7  |  Page 8  |  Page 9  |  Page 10  |  Page 11  |  Page 12  |  Page 13  |  Page 14  |  Page 15  |  Page 16  |  Page 17  |  Page 18  |  Page 19  |  Page 20  |  Page 21  |  Page 22  |  Page 23  |  Page 24  |  Page 25  |  Page 26  |  Page 27  |  Page 28  |  Page 29  |  Page 30  |  Page 31  |  Page 32  |  Page 33  |  Page 34  |  Page 35  |  Page 36  |  Page 37  |  Page 38  |  Page 39  |  Page 40  |  Page 41  |  Page 42  |  Page 43  |  Page 44  |  Page 45  |  Page 46  |  Page 47  |  Page 48  |  Page 49  |  Page 50  |  Page 51  |  Page 52  |  Page 53  |  Page 54  |  Page 55  |  Page 56  |  Page 57  |  Page 58  |  Page 59  |  Page 60  |  Page 61  |  Page 62  |  Page 63  |  Page 64  |  Page 65  |  Page 66  |  Page 67  |  Page 68  |  Page 69  |  Page 70  |  Page 71  |  Page 72  |  Page 73  |  Page 74  |  Page 75  |  Page 76