scholarly journals Scalable image processing techniques for quantitative analysis of volumetric biological images from light-sheet microscopy

2019 ◽  
Author(s):  
Justin Swaney ◽  
Lee Kamentsky ◽  
Nicholas B Evans ◽  
Katherine Xie ◽  
Young-Gyun Park ◽  
...  
Keyword(s):  
Image Processing ◽  
Quantitative Analysis ◽  
Parallel Processing ◽  
Light Sheet ◽  
Reference Image ◽  
Initial Alignment ◽  
Biological Images ◽  
Light Sheet Microscopy ◽  
Volumetric Images ◽  
Dataset Size

AbstractHere we describe an image processing pipeline for quantitative analysis of terabyte-scale volumetric images of SHIELD-processed mouse brains imaged with light-sheet microscopy. The pipeline utilizes open-source packages for destriping, stitching, and atlas alignment that are optimized for parallel processing. The destriping step removes stripe artifacts, corrects uneven illumination, and offers over 100x speed improvements compared to previously reported algorithms. The stitching module builds upon Terastitcher to create a single volumetric image quickly from individual image stacks with parallel processing enabled by default. The atlas alignment module provides an interactive web-based interface that automatically calculates an initial alignment to a reference image which can be manually refined. The atlas alignment module also provides summary statistics of fluorescence for each brain region as well as region segmentations for visualization. The expected runtime of our pipeline on a whole mouse brain hemisphere is 1-2 d depending on the available computational resources and the dataset size.

scholarly journals Hydrogel encapsulation of living organisms for long-term microscopy

2017 ◽  
Author(s):  
Kyra Burnett ◽  
Eric Edsinger ◽  
Dirk R. Albrecht
Keyword(s):  
Light Sheet ◽  
C Elegans ◽  
Light Sheet Microscopy ◽  
Confined Spaces ◽  
Single Cell Imaging ◽  
Volumetric Images ◽  
Living Organisms ◽  
Resolution Single ◽  
Hydrogel Encapsulation

AbstractImaging living organisms at high spatial resolution requires effective and innocuous immobilization. Long-term imaging, across development or behavioral states, places further demands on sample mounting with minimal perturbation of the organism. Here we present a simple and inexpensive method for rapid encapsulation of small animals of any developmental stage within a photocrosslinked polyethylene glycol (PEG) hydrogel, gently restricting movement within their confined spaces. Immobilized animals maintained a normal, uncompressed morphology in a hydrated environment and could be exposed to different aqueous chemicals. We focus in particular on the nematode C. elegans, an organism that is typically viewed with paralyzing reagents, nanobeads, adhesives, or microfluidic traps. The hydrogel is optically clear, non-autofluorescent, and nearly index-matched with water for use with light-sheet microscopy. We captured volumetric images of optogenetically-stimulated responses in multiple sensory neurons over 14 hours using a diSPIM light-sheet microscope, and immobilized worms were recoverable and viable after 24 hours encapsulation. We further imaged living pygmy squid hatchlings to demonstrate size scalability, characterized immobilization quality for various crosslinking parameters and identified paralytic-free conditions suitable for high-resolution single cell imaging. PEG hydrogel encapsulation enables continuous observation for hours of small living organisms, from yeast to zebrafish, and is compatible with multiple microscope mounting geometries.

scholarly journals Erratum: Live imaging and quantitative analysis of gastrulation in mouse embryos using light-sheet microscopy and 3D tracking tools

2014 ◽  
Vol 9 (10) ◽  
pp. 2513-2513 ◽  
Author(s):  
Takehiko Ichikawa ◽  
Kenichi Nakazato ◽  
Philipp J Keller ◽  
Hiroko Kajiura-Kobayashi ◽  
Ernst H K Stelzer ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Light Sheet ◽  
Live Imaging ◽  
Mouse Embryos ◽  
3D Tracking ◽  
Light Sheet Microscopy

Live imaging and quantitative analysis of gastrulation in mouse embryos using light-sheet microscopy and 3D tracking tools

2014 ◽  
Vol 9 (3) ◽  
pp. 575-585 ◽  
Author(s):  
Takehiko Ichikawa ◽  
Kenichi Nakazato ◽  
Philipp J Keller ◽  
Hiroko Kajiura-Kobayashi ◽  
Ernst H K Stelzer ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Light Sheet ◽  
Live Imaging ◽  
Mouse Embryos ◽  
3D Tracking ◽  
Light Sheet Microscopy

scholarly journals The Applications of Lattice Light-sheet Microscopy for Functional Volumetric Imaging of Hippocampal Neurons in a Three-Dimensional Culture System

Micromachines ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 599 ◽  
Author(s):  
Chen ◽  
Liu ◽  
Lu ◽  
Lee ◽  
Tsai ◽  
...  
Keyword(s):  
Cell Culture ◽  
Hippocampal Neurons ◽  
Three Dimensional ◽  
Light Sheet ◽  
Three Dimensions ◽  
Laser Exposure ◽  
Spatiotemporal Resolution ◽  
Strong Light ◽  
Light Sheet Microscopy ◽  
Volumetric Images

The characterization of individual cells in three-dimensions (3D) with very high spatiotemporal resolution is crucial for the development of organs-on-chips, in which 3D cell cultures are integrated with microfluidic systems. In this study, we report the applications of lattice light-sheet microscopy (LLSM) for monitoring neuronal activity in three-dimensional cell culture. We first established a 3D environment for culturing primary hippocampal neurons by applying a scaffold-based 3D tissue engineering technique. Fully differentiated and mature hippocampal neurons were observed in our system. With LLSM, we were able to monitor the behavior of individual cells in a 3D cell culture, which was very difficult under a conventional microscope due to strong light scattering from thick samples. We demonstrated that our system could study the membrane voltage and intracellular calcium dynamics at subcellular resolution in 3D under both chemical and electrical stimulation. From the volumetric images, it was found that the voltage indicators mainly resided in the cytosol instead of the membrane, which cannot be distinguished using conventional microscopy. Neuronal volumetric images were sheet scanned along the axial direction and recorded at a laser exposure of 6 ms, which covered an area up to 4800 μm2, with an image pixel size of 0.102 μm. When we analyzed the time-lapse volumetric images, we could quantify the voltage responses in different neurites in 3D extensions.

scholarly journals Application of light sheet microscopy for qualitative and quantitative analysis of bronchus-associated lymphoid tissue in mice

2018 ◽  
Vol 15 (10) ◽  
pp. 875-887 ◽  
Author(s):  
David Twapokera Mzinza ◽  
Henrike Fleige ◽  
Kristin Laarmann ◽  
Stefanie Willenzon ◽  
Jasmin Ristenpart ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Lymphoid Tissue ◽  
Light Sheet ◽  
Qualitative And Quantitative Analysis ◽  
Qualitative And Quantitative ◽  
Light Sheet Microscopy

scholarly journals Quantitative Analysis of Embryogenesis: A Perspective for Light Sheet Microscopy

2012 ◽  
Vol 23 (6) ◽  
pp. 1111-1120 ◽  
Author(s):  
Burkhard Höckendorf ◽  
Thomas Thumberger ◽  
Joachim Wittbrodt
Keyword(s):  
Quantitative Analysis ◽  
Light Sheet ◽  
Light Sheet Microscopy

Interactive multiple area spectrum integration (MASI)

1994 ◽  
Vol 52 ◽  
pp. 942-943
Author(s):  
John A. Hunt ◽  
Richard D. Leapman ◽  
David B. Williams
Keyword(s):  
Image Processing ◽  
Low Dose ◽  
Routine Analysis ◽  
Reference Image ◽  
Area Spectrum ◽  
List Type ◽  
Type Number ◽  
Image Processor ◽  
X Ray ◽  
Scanning Path

Interactive MASI involves controlling the raster of a STEM or SEM probe to areas predefined byan integration mask which is formed by image processing, drawing or selecting regions manually. EELS, x-ray, or other spectra are then acquired while the probe is scanning over the areas defined by the integration mask. The technique has several advantages: (1) Low-dose spectra can be acquired by averaging the dose over a great many similar features. (2) MASI can eliminate the risks of spatial under- or over-sampling of multiple, complicated, and irregularly shaped objects. (3) MASI is an extremely rapid and convenient way to record spectra for routine analysis. The technique is performed as follows:Acquire reference imageOptionally blank beam for beam-sensitive specimensUse image processor to select integration mask from reference imageCalculate scanning path for probeUnblank probe (if blanked)Correct for specimen drift since reference image acquisition

Development of New Image Registration Techniques – A Research Framework

2018 ◽  
Vol 8 (3) ◽  
pp. 50
Author(s):  
Sindhu Madhuri G. ◽  
Indira Gandhi M P
Keyword(s):  
Image Processing ◽  
Image Registration ◽  
Digital Image Processing ◽  
Digital Image ◽  
Creative Thinking ◽  
Reference Image ◽  
Transformation Technique ◽  
Research Framework ◽  
Registration Process ◽  
Data Source

Image is a basic and fundamental data source for the digital image processing. This image data source is required to be processed into information or intelligence and further to knowledge levels where it is required to understand and migrate into knowledge economy systems. Image registration is one of such key and most important process already identified in the digital image processing domain. Image registration is a process of bringing the reference image and sensed image into a common co-ordinate system, and application of complex transformation techniques for necessary comparison of reference with sensed images obtained from different - views, times, spaces, etc., in order to extract the valuable information and intelligence embedded in them. Due to the complexity of overall image registration process, it is difficult to suggest a single transformation technique even for a specific application. In addition, it is highly impossible to suggest one single transformation technique for comparison of various sensed images with a reference image during the image registration process. This research gap calls for the development of new image registration techniques for the application of more than one transformation technique during the image registration process for the necessary comparisons with reference image & sensed images, those are obtained from the available heterogeneous sources or sensors, based on the requirement. In addition, it is a basic need to attempt for the measurement of effectiveness of the image registration process also. Therefore, a research framework is developed for image registration process and attempted for the measurement of its effectiveness also. This new research area is a novel idea, and is expected to emerge as a provision for the knowledge computations with creative thinking through the embedded intelligence extraction during the complex image registration process.

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