AnalyzeDirect Abbie S.Ireland et al. MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate. Cancer Cell.
Publication Date
May 30, 2020
How Analyze was Used
“To determine tumor burden, resulting images were processed with Analyze 11.0 software (Analyze Direct) as described previously (Mollaoglu et al., 2017). Scans were calibrated for Hounsfield Units (HU) by determining the mean value of ‘‘Bed’’ and ‘‘Air’’ for representative scans through the region of interest (ROI) tool and matching those values to their known HU (40 HU and -1000 HU, respectively) using the ‘‘Image Algebra’’ tool. Every image was then applied a 3x3x3 Median Filter from the ‘‘Spatial Filters’’ window. Thresholds of ‘‘Air’’ vs. ‘‘Dense Tissue’’ were established using the ROI and histogram tools. For tumor burden analysis, the object map was created using the previously established thresholds; adjustments were made manually using ‘‘Spline Edit’’, ‘‘Draw’’, ‘‘Trace’’ and ‘‘Nudge Edit’’ tools. With the ‘‘Morphology’’ tool, the object map was made binary by using the threshold morphing tool. Then, the map was dilated 3 times using 5x5x5 Jack-shaped structuring elements. The holes were then filled on every 2D-orientation. The map was finally brought back to its original size using the ‘‘Erode’’ tool 3 times using 5x5x5 Jack-shaped structuring elements. The volumetric analyses were then performed in the ROI window using the pre-established thresholds and non-airspace was
calculated using the formula: Non- airspace = 1 – (VolAir/ROIVol).”
Keywords
SCLC, Neuroendocrine, Tumor evolution, Plasticity, MYC, NOTCH, ASCL1, NEUROD1, Mouse models, YAP1
Author Affiliation(s)
University of Utah, Salt Lake City, Utah, USA
