Computational protocol: An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes

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Protocol publication

[…] 3D images were obtained by stacking up and aligning 2D image slices based on minimizing the mean squared error (MSE) between aligned regions in consecutive slices using a custom MATLAB code and XUVStitch (http://www.xuvtools.org). All surface generated images and videos of original data or surface generated data were created using IMARIS software (Bitplane).Raw quantification data were extracted by using MATLAB, and statistical analysis was performed in R studio. P < 0.05 (two-tailed) was considered statistically significant. […]

Pipeline specifications

Software tools XuvTools, Imaris
Application Laser scanning microscopy
Diseases Neoplasms