Biological Applications
Te Fractal and GLCM Textural Parameters of Chromatin May Be Potential Biomarkers of Papillary Tyroid Carcinoma in Hashimoto’s Tyroiditis Specimens by M Dinčić, J Todorović, J Nešović Ostojić, S Kovačević, D Dunđerović, S Lopičić, S Spasić, S Radojević-Škodrić, D Stanisavljević, and AŽ Ilić, Microsc Microanal | doi:10.1017/S1431927620001683
papillary thyroid carcinoma (PTC) is sometimes hindered due to sharing of
Accurate diagnosis of Hashimoto’s thyroiditis (HT) and similar nuclear features. Quantification of
the
differences between HT-associated PTC (HT/PTC) versus HT alone specimens can facilitate diagnosis and reduce inaccurate diagnosis due to the subjective experience of an observer. We analyzed 250 segmented nuclei per group (25 nuclei per patient, 10 patients per group) using ImageJ soſtware (NIH, Bethesda, MD, USA) for fractal analysis and an in-house written code for the gray-level co-occurrence matrix (GLCM) analysis (Figure). Malignant cells from the HT/PTC specimens showed lower chromatin fractal dimension (p=0.0321) and higher lacunarity (p=0.0038) compared to corresponding cells from the HT alone specimens. Additionally, we observed statistically significant differences for the five studied GLCM features: Contrast, Correlation, Angular second moment, Homogeneity, and Entropy. Te differences in visual textures of follicular cell chromatin could be used for improved evaluation of distinctive features of HT/ PTC versus HT in cytology and surgical pathology specimens.
Techniques Development
Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post Acquisition Data Processing, Visualisation, and Structural Characterisation by GW Paterson, RWH Webster, A Ross, KA Paton, TA Macgregor, D McGrouther, I MacLaren, and M Nord, Microsc Microanal | doi:10.1017/S1431927620024307
New generations of radiation hard fast pixelated detectors
incorporating direct electron technologies are revolutionizing aspects of scanning transmission electron microscopy (STEM). Tis has led to the burgeoning field of four-dimensional STEM (4D-STEM), where a slice of reciprocal space is recorded in high dynamic range and with low or zero readout noise at each probe position. Tis allows a multitude of analyses to be performed, with the potential of yielding greatly improved insights into a range of samples. We report two open source Python soſtware libraries (fpd and PixStem) to enable the efficient processing and visualization of 4D-STEM data, and cover aspects of their use in performing STEM characterization of the structural properties of materials. Examples are given of virtual detector imaging, higher order Laue zone analysis, nanobeam electron diffraction, and scanning precession electron diffraction (Figure). In the latter, we demonstrate excellent nanoscale lattice parameter mapping with a precision ≤ 0.06%. Extensive documentation is provided online, and all data and scripts used in the article are publicly available.
66 doi:10.1017/S1551929520001273
Nine parameters obtained using fractal and GLCM textural analysis showed significant differences in the visual textures of chromatin in HT/PTC versus the HT alone specimens.
Processing steps of the lattice parameter extraction from 4D-STEM data from an MgO substrate acquired in SPED mode.
www.microscopy-today.com • 2020 September
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