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3D Visualizer Workflow

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DMC-416-/ edited this page Aug 21, 2022 · 29 revisions

3D visualizer

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.

vieww Figure 1: Three-channel CLSM image is rendered into a volume using a volume rendering algorithm.

What types of input files does our 3D visualization platform accepts?

  • 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.

2 Figure 2: Shows the process of file conversion between raw and DICOM.

How to use our 3D visualizer to visualize microscope imaging modalities data in 3D?

  • Below you will find the steps about how to use it:

    1. RAW to DICOM:

      • 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.

    2. Selection of the viewer:

      • Secondly, before uploading files/folders into the system, users must determine how or which viewer they wish to use to visualize their data. Three viewers are provided, each with its unique input intake functions and visualization features. When using the 3D viewer, users may upload several files by manually entering numbers in the select the number of inputs field or spinning the wheel, but in the case of tri-planar and MPR viewers, users are allowed to upload only one file/folder at a time.

      For example, to utilize a volume rendering viewer, follow these steps:

      • First, choose the 3D option (if the 3D option is selected then the other two tri-planar and MPR options will be disabled).

        3D-1

      • In the second step, select volume rendering instead of surface since we will be visualizing our data in 3D volume space in this example.

        vol-1

      • In the third stage, the user must first determine how many files/folders they want to upload (the system always excepts one file by default, and if the user uploads two files without increasing the select the number of inputs field to 2,3,... etc., an error will occur in the promise, and then the web-page will be reloaded).

        1. Default scenario > upload just one folder: Click the Choose Files option, upload only one folder, and then hit Render. Users can alter the colour code before or after the image is rendered, therefore changing it at the beginning is not necessary.

        vol-2

        1. For two inputs > upload just two folders: Click the Choose Files option and upload the first folder; similarly, press it again to upload the second folder; after both data have been uploaded one by one, press the render button (if the user did not upload the files correctly, then the system will display an error related to Promise, indicating that the user was required to upload two distinct data but only upload one data).

        vol-3

        1. For ten inputs > upload ten folders: By following the same steps as described in (a) (b), the user can be able to upload ten files.

        vol-4

        1. A complete representation of how the volume platform would appear if the user uploads ten image data folders.

        vol-5

        1. By following the above steps, now we will visualize a four-channel CLSM image into a volume rendering viewer.

        vol-6 Figure 3: Four-channel CLSM image is rendered into a volume using a volume rendering algorithm.

        Likewise, the user can follow the same above-described steps to visualise their data in the surface, tri-planar, and MPR viewer.

    3. Features:

       1. Volume rendering viewer consists of four features: Image visibility on/off, opacity slider, sample distance slider, and colour.
 2. Surface rendering viewer consists of four features: Image visibility on/off, opacity slider, Iso-value slider, and colour.

Reference:

  1. 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
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