Computational protocol: Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy

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Protocol publication

[…] Measured TXM images were cropped and further processed by Java-based image processing and analysis software (ImageJ 1.41n,, Wayne Rasband, NIH, USA). The IMOD tomography package was used to align and reconstruct of images acquired from −30° to 50° with step 10°. Defect points in PCs were used for aligning and tracking to 3D reconstruct. Reconstruction was performed by a weighted back-projection algorithm in IMOD package. […]

Pipeline specifications

Software tools ImageJ, IMOD
Application Microscopic phenotype analysis
Organisms Dipturus trachyderma
Diseases Coproporphyria, Hereditary
Chemicals Polystyrenes