Siddiqui, O. | Search bioRxiv

bioRxiv2019

Chromosome 17: neXt-MP50 C-HPP Challenge Completed

The C-HPP Team for Chromosome 17 has documented meeting the neXt-MP50 Missing Protein Challenge. Protein-level PE1 evidence including MS and protein-protein interaction data from the global proteomics community has reduced the number of PE2,3,4 proteins coded on Chromosome 17 by 50 since the 2016 baseline in neXtProt. As a follow-up to our analysis and prioritization of Chr 17 missing proteins last year, we describe what predictions and guidance were successful in this update and we explain the dynamics of a net reduction of PE2,3,4 Missing Proteins. This analysis can serve as a guide for other C-HPP chromosome teams seeking high-quality evidence for the 2129 remaining missing proteins.

systems biology↗

bioRxiv2019

OptiJ: Open-source optical projection tomography of large organ samples

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 m resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.

biophysics↗