This page contains a Flash digital edition of a book.
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 ( ) 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.


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.


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 • 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