7,346 research outputs found
An automated workflow for parallel processing of large multiview SPIM recordings
Multiview light sheet fluorescence microscopy (LSFM) allows to image
developing organisms in 3D at unprecedented temporal resolution over long
periods of time. The resulting massive amounts of raw image data requires
extensive processing interactively via dedicated graphical user interface (GUI)
applications. The consecutive processing steps can be easily automated and the
individual time points can be processed independently, which lends itself to
trivial parallelization on a high performance cluster (HPC). Here we introduce
an automated workflow for processing large multiview, multi-channel,
multi-illumination time-lapse LSFM data on a single workstation or in parallel
on a HPC. The pipeline relies on snakemake to resolve dependencies among
consecutive processing steps and can be easily adapted to any cluster
environment for processing LSFM data in a fraction of the time required to
collect it.Comment: 13 pages with supplement, LATEX; 1 table, 1 figure, 2 supplementary
figures, 2 supplementary lists, 2 supplementary tables; corrected error in
results table, results unchange
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
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