If you work for academic, government, or non-profit institutions you may download and use this software for free. We only ask that you acknowledge the use of these programs in your published papers, talks, and reports. We also ask that you reference the key scientific publications where the algorithms behind the programs are described.
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In the biomedical sciences, a versatile tool allowing visualization-based analysis for many-channel data is crucial for researchers to decipher fluorescence microscopy scans, perform qualitative and quantitative data analysis, and present outcomes. The challenges are twofold from a software development perspective. 1) Volumes from a many-channel data set need to be combined or intermixed for viewing, but intensity values of each channel need to be preserved for interactive adjustment, editing, and analysis. These requirements minimize the benefits of preprocessing in Amira and Vaa3D as channel data processing becomes dynamic and dependent on user inputs. 2) Freehand analysis tools, such as the paintbrush in FluoRender, require real-time processing, which has been achieved by using GPUs. However, hardware resources within a GPU are limited, making it impractical to use many texture units, as in Imaris. It is essential to rethink and redesign the basic data model for handling channels for accurate, efficient, and versatile visualization-analysis workflows. Here, we present a thorough reconstruction of our original software tool, FluoRender [3], achieving a joint freehand segmentation and visualization tool for many-channel fluorescence data. Compared to the original tool, which supported fewer than 10 channels, the upgrade significantly extends the capacity for multichannel data and addresses the two challenges in a many-channel setting. The new FluoRender uses the latest graphics application programming interfaces (APIs) to integrate intuitive analysis functions with interactive visualization for multichannel data and ensures future extensions for sophisticated visualization-based data analysis.
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