3D Visualizer Workflow
We developed an open-source web-based multidimensional 3D visualizer to visualize the 3D nature of imaging obtained from confocal laser scanning and focused-ion beam electron microscopy modalities on any web browser. In our 3D visualizer platform, we have implemented three distinct visualizers: 1). 3D (three-dimensional view), 2). Tri-Planar (cross-sectional view), and 3). MPR (orthogonal viewer). The 3D viewer is further separated into two viewers: i). Volume and ii). Surface rendering.
- As we all know, there is no data file format standardization in the microscope field, as there is in the medical industry, and our previous study discovered that there are more than dozens of file formats in the microscope field, and designing a visualizer for each file format is not viable. As a result, to reduce interoperability issues between scanners while also reducing proprietary issues within their file formats, we previously developed a conversion pipeline [1] that efficiently converts confocal laser scanning and focused ion beam electron microscope imaging modalities into DICOM file standards. Therefore, in a conclusion, our visualizer intakes a series of DICOM files as input.
- Below you will find the steps about how to use it:
- At the very first step, the user needs to convert their raw data files into DICOM standard format if they are not already in DICOM format. There are open-source packages available to accomplish this, such as the OME-Bioformats library, which can read microscope imaging raw data files, and the Pydicom library, which can read/write DICOM files.
Reference:
- Gupta, Yubraj, Carlos Costa, Eduardo Pinho, and Luís Bastião Silva. 2022. "DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners" Sensors 22, no. 6: 2322. https://doi.org/10.3390/s22062322