title: Review of free software tools for image analysis of fluorescence cell micrographs.
abstract: An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand-alone, Matlab-based, ImageJ-based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure-ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure-ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well-structured menu and intuitive graphical user interface.
authors.affiliation: Fraunhofer Institute for Integrated Circuits IIS, Erlangen, Germany.
authors.forename: V
authors.initials: V
authors.lastname: Wiesmann
authors.forename: D
authors.initials: D
authors.lastname: Franz
authors.forename: C
authors.initials: C
authors.lastname: Held
authors.forename: C
authors.initials: C
authors.lastname: Münzenmayer
authors.forename: R
authors.initials: R
authors.lastname: Palmisano
authors.forename: T
authors.initials: T
authors.lastname: Wittenberg
mesh_terms: D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008856:Microscopy, Fluorescence; D012984:Software
keywords: Cell segmentation; fluorescence microscopy; image analysis; software; usability