Visualizing Lung Bronchus Microstructure

To create the charts and movies, we used the Amira software (version 2020.1, FEI, Merignac Cedex, France) and the Imaris software (version 9.7.2, bitplane, Switzerland) to visualize the dataset. Amira software was used to import the preprocessed dataset using a desktop graphical workstation (7920 with one Intel Xeon Gold 6226R CPU, 512 GB memory and an Nvidia GeForce RTX 3090 graphics card, Dell Inc., Round Rock, Texas, USA). We used the OTSU thresholding technique in conjunction with manually corrected parameters on the red channel cytoarchitecture pictures to reconstruct the bronchus. Amira was used to convert the TIFF data format to the native LDA type so that the TB-sized data could be processed on a single workstation. The extraction of the data in the range of interest, sampling or interpolation, reslicing of the images, determination of the maximum intensity projection, volume and surface rendering, and creation of movies using Amira's main module were all steps in the visualization process [30 (link), 31 (link)].

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Li X., Zhang B., Liang Y, & Li T. (2023). Multiscale reconstruction of bronchus and cancer cells in human lung adenocarcinoma. BioMedical Engineering OnLine, 22, 11.

Publication 2023

Amira software

Bronchus Cedex Gold Memory

Corresponding Organization : Nankai University

Other organizations : Tianjin Chest Hospital, Tianjin University, Chinese Academy of Medical Sciences & Peking Union Medical College

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Variable analysis

independent variables

Use of Amira software (version 2020.1, FEI, Merignac Cedex, France)
Use of Imaris software (version 9.7.2, bitplane, Switzerland)

dependent variables

Visualization of the dataset
Reconstruction of the bronchus
Conversion of TIFF data format to the native LDA type
Extraction of data in the range of interest
Sampling or interpolation
Reslicing of the images
Determination of the maximum intensity projection
Volume and surface rendering
Creation of movies

control variables

Desktop graphical workstation (7920 with one Intel Xeon Gold 6226R CPU, 512 GB memory and an Nvidia GeForce RTX 3090 graphics card, Dell Inc., Round Rock, Texas, USA)

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