Open-Source Software
individuals.) T is enables the user to easily reposition the current fi eld of view to match images between two experiments. SciScript Module . SciScript is a scripting feature that provides a macro-like functionality ( Figure 3 ), allowing the user to automate repetitive tasks that would otherwise need to be carried out manually via the main SciScan GUI. Macro fi les are stored in a human readable format and can be generated and edited either via the SciScript GUI, by using a simple text editor, or by generating a text fi le from other programming environments. SciScript pre-sets are available to auto-generate macros for commonly used experimental sequences. T e Slow Z Stack pre-set creates a macro representation of the data that has been set up in the z -stack table. It converts each plane into a discrete 2D acquisition to ensure accurate objective positioning and improved imaging stability. T e macro will step between each plane before adjusting the laser power as specifi ed in the table and executing the 2D scan. Separate 2D images are recorded as raw fi les into a temporary folder, aſt er completion of the macro the images are recombined and saved into the standard root folder with a batch fi le to open the combined raw image in ImageJ [ 12 ]. T e Image Tiling pre-set allows users to automatically collect multiple 2D or 3D acquisitions across a predefi ned region for post hoc mosaic stitching. Active X connectivity . ActiveX connectivity allows the user to control SciScan from programming languages such as MATLAB or Python. It provides easy access to basic SciScan functions (start/stop recording, adjust scan parameters, control stage motion, etc.) but also caters to advanced automation requirements. In fact, any variable used within SciScan can be accessed, not only via the GFG methods within LabVIEW, but also via ActiveX from external programming environments. OME compatibility . SciScan supports the OME’s XML and OME-TIFF formats. T is allows users to load, organize,
and analyze data with the Bio-Formats Java library. T e OME (
https://www.openmicroscopy.org ) is a consortium of academic laboratories and commercial entities that create open tools to support data management for biological light microscopy. T ey have created the OME Model, a specifi cation for storing biological imaging data including a wide variety of picture, acquisition, and experimental parameters [ 11 ]. T is enables the simple exchange of imaging data between diff erent soſt ware packages. T e OME-XML is a fi le format used to store metadata per the OME model in an XML fi le, which can be shared easily among diff erent sites and users. T e OME-TIFF is a multi-page tiff fi le that contains the OME metadata within the header as OME-XML. T e pixels of the OME-TIFF fi le can be read by any TIFF-compatible programm, and the metadata can be extracted with an OME-aware application. T e ability to save imaging data as an OME-TIFF or with an
OME-XML fi le allows users to open, organize, and share metadata in a fully standardized format. T is helps researchers to dissem- inate and analyze data in other soſt ware, compare their data with others using the OME Model, and keep track of where and how the images were acquired. In addition, the OME consortium currently has two major tools to help those working with OME-XML and OME-TIFF fi les: (a) Bio-Formats, a library containing many features related to OME-XML, including conversion of third- party metadata into the OME-XML structure and (b) OMERO, a server that can import OME-XML and OME-TIFF data and export OME-TIFF fi les, providing research groups with a means of cataloging and storing imaging data on a central server.
Results
Figure 3 : SciScript Module provides a macro-like functionality, allowing the user to automate repetitive tasks. Presets are available to auto-generate macros for commonly used experimental sequences.
14
Several of the functions described above are currently in use in labs around the world. T us, SciScan is enabling neuroscien- tists to pursue complex questions. Position Save Module . Dr. Sabine Liebscher at the Ludwig- Maximilians-Universität München uses the Position Save Module within SciScan to perform chronic in vivo imaging in mice. Using a Scientifi ca Multiphoton Resonant System, a fi duciary marker such as a crossing or branching of blood vessels is stored as the “origin” ( Figure 4 ). T is point is easily relocated during each imaging session and can be aligned to the image taken at an earlier time point. T e coordinates of all imaging regions are stored relative to the origin, making it easy to relocate and image the same region days or weeks apart. T is enables Dr Liebscher’s lab to ask questions about changes in function of the same neurons over long time periods. SciScript Module . Dr. Jonathan Taylor from the University of Glasgow is currently working on a SciScript macro that will enable the microscope to create a 3D image stack of a beating zebra fi sh heart as
www.microscopy-today.com • 2017 September
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