BISE is set up as a knowledge aggregation site that points to other established community-based efforts that host solutions for image analysis problems. In this sense, the system is able to capitalise on already existing active scientific communities but through the lens of specific bioimaging vocabulary. As stated on the website, code and software is never hosted on the platform – it is a central hub. Instead of the time-consuming task of searching each of the many software-specific repositories (and discussion forums), a BISE query can be used to point the user to specific sites such as GitHub or MathWorks File Exchange, with the added confidence of expert content curation. A search of BISE will also likely have returned a list of solutions and even a comparison of the different existing implementations (and their history).
Another crucial factor for BISE users would be the licensing terms of available products – whether software is open source or available commercially. BISE will help users find the exact solution suitable for their needs and laboratory licensing capabilities.
Furthermore, by making metrics and statistics available for each curated entry, users should be able to track where the most active and engaged software development is happening. This will not only reveal website traffic information, but more significantly, the scientific trends and research interests as they emerge.
The most common platforms referenced and curated in BISE (as of April 2018) are shown in the table below [DATA NEEDED]:
SoftwareNo. of EntriesLanguageLicense‘Home’
MATLABxxxMATLABCommercialMathworks File Exchange
ImageJxxxJavaImageJ MacrosFree & Open SourceImageJ Forum (with new efforts to combine with CellProfiler Forum)
etc etc…
Consider the perspective of a biologist who needs to track fluorescently labeled ends of growing and shrinking microtubules, acquired with confocal microscope as a multi-channel time-series of z-stacks (3D), the solution sought should be semi-automatic, open-source, and exist as an ImageJ/Fiji plugin. By entering the underlined keywords in BISE, a detailed response with the following details can be acquired:
[Consider a FIGURE representing this exact search query? Screenshot? Behind-the-scenes explanation?] Relationship with code repository, forum other sites… some are from sup materials of papers, some from github etc…Showing graphically how BISE is in the middle and provided link to code repositories (GitHub, File Exchange, Bitbucket), journal suppl. material sites, article DOIs, Figshare, University hosted sites with tool descriptions, websites for online analysis, personal websites with code description, commercial software websites, etc