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Figure 2 : User interface for SciScan’s position save module, which enables users to store multiple positions of their XY stage and Z focus motor and to easily recall them at a later date.


for processing and analyzing data. T us, SciScan directly connects the data acquisition process with the data pipeline or workfl ow, allowing full automation of the entire process. Furthermore, imaging data recorded with SciScan is compatible with the Open Microscopy Environment (OME) such that images and metadata can be imported into OME-capable soſt ware without the need for proprietary import fi lters [ 11 ].


Materials and Methods Concept and framework . SciScan is based on the idea of providing the scientifi c community with a LabVIEW-based soſt ware LSM that is open-source, free of charge, and highly modular. To this end, we chose a design pattern based on a functional global variable (FGV) in which variables of data type “Variant” can be stored. T e Variant data type can contain strings, numerics, Booleans, arrays, clusters, refnums, or any other data type available in LabVIEW. T erefore, we refer to this FGV as a Generalized Functional Global (GFG), a concept that was previously suggested by a user on the LabVIEW Idea Exchange forum ( http://scien.se/GFG-Sci ).


We have expanded this idea such that any change of a GFG variable automatically triggers an event, which can be listened for in other stand-alone, top-level virtual instruments (VIs). T is facilitates easy communication between modules with minimal overhead. End users can write custom modules that can access the GFG either by using set or get methods or by listening for variable change events. T us, new function- ality can be added without modifying any of the existing code itself. T is is conceptually like LabVIEW object-oriented programming (LVOOP), but it avoids the steep learning curve,


2017 September • www.microscopy-today.com


which researchers without a background in computer science oſt en experience with LVOOP. Functionality . SciScan can be used to control and acquire data from both galvanometer and resonant LSMs. A graphical user interface (GUI) provides control over all the features commonly found in LSM soſt ware ( Figure 1 ), such as two-dimensional frame scans, z stacks, arbitrary line scans (Galvo only), zoom (digital and optical), on-the-fl y plotting of mean gray values of multiple regions of interest (ROIs), and controls for piezoelectric focusing devices to facilitate fast 3D scanning, among others. Furthermore, SciScan provides functionality that is rarely found in other LSM soſt ware packages, such as the Position Save Module, the SciScript Module, ActiveX connectivity, and OME compatibility. Position Save Module . T e Position Save Module allows users to store multiple positions of their XY stage and Z focus motor and easily recall them later. T is is a crucial function- ality for long-term in vivo imaging studies. Points of interest are saved relative to a user-defi ned origin, usually an easily identifi able landmark (for example, a meningeal blood vessel pattern). A reference image for each position is also stored. It is not unusual that the absolute position of the origin changes slightly between experimental days (due to the practicalities of positioning a live specimen), in which case the user can easily reassign the absolute position of the origin landmark. All stored points of interest will automatically be corrected accordingly. Furthermore, positions can be manually fi ne-tuned using the “overlay” function, whereby the stored image and the current live image are displayed as a red/green overlay image. ( Figure 2 shows a red/blue overlay image suitable for some color-blind


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