Imaging the Intestinal Transcriptome With Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH).

Multiplexed error-robust fluorescence in situ hybridization (MERFISH) is a massively multiplexed single RNA-molecule imaging technique capable of spatially resolved single-cell transcriptomic profiling of thousands of genes in millions of cells within intact tissue slices. Initially introduced for brain tissues, MERFISH has since been extended to other tissues, where rapid RNA degradation during the preparation process can pose challenges. This protocol outlines the application of MERFISH in one such challenging tissue, the mammalian gastrointestinal tract.

Calculation of alpha particle single-event spectra using a neural network.

Introduction: A neural network was trained to accurately predict the entire single-event specific energy spectra for use in alpha-particle microdosimetry calculations.

Methods: The network consisted of 4 inputs and 21 outputs and was trained on data calculated using Monte Carlo simulation where input parameters originated both from previously published data as well as randomly generated parameters that fell within a target range. The 4 inputs consisted of the source-target configuration (consisting of both cells in suspension and in tissue-like geometries), alpha particle energy (3.

Technical note: TIGRE-DE for the creation of virtual monoenergetic images from dual-energy cone-beam CT.

Background: Dual-energy (DE)-CBCT represents a promising imaging modality that can produce virtual monoenergetic (VM) CBCT images. VM images, which provide enhanced contrast and reduced imaging artifacts, can be used to assist in soft-tissue visualization during image-guided radiotherapy.

Purpose: This work reports the development of TIGRE-DE, a module in the open-source TIGRE toolkit for the performance of DE-CBCT and the production of VM CBCT images.

Development and implementation of an automated and highly accurate reporting process for NGS-based clonality testing.

B and T cells undergo random recombination of the VH/DH/JH portions of the immunoglobulin loci (B cell) and T-cell receptors before becoming functional cells. When one V-J rearrangement is over-represented in a population of B or T cells indicating an origin from a single cell, this indicates a clonal process. Clonality aids in the diagnosis and monitoring of lymphoproliferative disorders and evaluation of disease recurrence.

Effect of scattered megavoltage x-rays on markerless tumor tracking using dual energy kilovoltage imaging.

Purpose: To determine the effect of megavoltage (MV) scatter on the accuracy of markerless tumor tracking (MTT) for lung tumors using dual energy (DE) imaging and to consider a post-processing technique to mitigate the effects of MV scatter on DE-MTT.

Methods: A Varian TrueBeam linac was used to acquire a series of interleaved 60/120 kVp images of a motion phantom with simulated tumors (10 and 15 mm diameter). Two sets of consecutive high/low energy projections were acquired, with and without MV beam delivery.