scholarly journals VisBio: a Flexible Open-Source Visualization Package for Multidimensional Image Data

2006 ◽  
Vol 14 (3) ◽  
pp. 6-11
Author(s):  
Curtis T. Rueden ◽  
Kevin W. Eliceiri
Keyword(s):  
Open Source ◽  
Curve Fitting ◽  
Image Data ◽  
Time Lapse ◽  
Dramatic Improvement ◽  
Exponential Curve ◽  
Lifetime Imaging ◽  
The Past ◽  
Resultant Data ◽  
Fitting Algorithm

Over the past few years there has been a dramatic improvement in microscopy acquisition techniques, in effective imaging modalities as well as raw hardware performance. As the microscopist's available tools become more sophisticated and diverse—e.g., time-lapse, Z sectioning, multispectra, lifetime, nth harmonic, polarization, and many combinations thereof—we face a corresponding increase in complexity in the software for understanding and interpreting the resultant data. With lifetime imaging, for example, it is overwhelming to study the raw numbers; instead, an exponential curve-fitting algorithm must be applied to extract meaningful lifetime values from the mass of photon counts recorded by the instrument.

scholarly journals Utilizing Social Media and Video Games to Control #DIY Microscopes

2016 ◽  
Author(s):  
Maxime Leblanc-Latour ◽  
Craig Bryan ◽  
Andrew Pelling
Keyword(s):  
Social Media ◽  
Open Source ◽  
Video Game ◽  
Low Cost ◽  
Image Data ◽  
Time Lapse ◽  
Raspberry Pi ◽  
Laboratory Equipment ◽  
User Input ◽  
Web Camera

ABSTRACTOpen-source lab equipment is becoming more widespread with the popularization of fabrication tools such as 3d-printers, laser cutters, CNC machines, open source microcontrollers and open source software. Although many pieces of common laboratory equipment have been developed, software control of these items is sometimes lacking. Specifically, control software that can be easily implemented and enable user-input and control over multiple platforms (PC, smartphone, web, etc.). The aim of this proof-of-principle study was to develop and implement software for the control of a low-cost, 3d-printed microscope. Here, we present two approaches, which enable microscope control by exploiting the functionality of the social media platform Twitter or player actions inside of the videogame Minecraft. The microscope was constructed from a modified web-camera and implemented on a Raspberry Pi computer. Four aspects of microscope control were tested, including single image capture, focus control and time-lapse imaging. The Twitter-embodiment enabled users to send “tweets” directly to the microscope. Image data acquired by the microscope was then returned to the user through a Twitter reply and stored permanently on the photo-sharing platform Flickr, along with any relevant metadata. Local control of the microscope was also implemented by utilizing the video game Minecraft, in situations where Internet connectivity is not present or stable. A virtual laboratory was constructed inside the Minecraft world and player actions inside the laboratory were linked to specific microscope functions. Here, we present the methodology and results of these experiments and discuss possible limitations and future extensions of this work.

scholarly journals Utilizing social media and video games to control #DIY microscopes

2017 ◽  
Vol 3 ◽  
pp. e139
Author(s):  
Maxime Leblanc-Latour ◽  
Craig Bryan ◽  
Andrew E. Pelling
Keyword(s):  
Social Media ◽  
Open Source ◽  
Video Game ◽  
Low Cost ◽  
Image Data ◽  
Time Lapse ◽  
Raspberry Pi ◽  
Laboratory Equipment ◽  
User Input ◽  
Web Camera

Open-source lab equipment is becoming more widespread with the popularization of fabrication tools such as 3D printers, laser cutters, CNC machines, open source microcontrollers and open source software. Although many pieces of common laboratory equipment have been developed, software control of these items is sometimes lacking. Specifically, control software that can be easily implemented and enable user-input and control over multiple platforms (PC, smartphone, web, etc.). The aim of this proof-of principle study was to develop and implement software for the control of a low-cost, 3D printed microscope. Here, we present two approaches which enable microscope control by exploiting the functionality of the social media platform Twitter or player actions inside of the videogame Minecraft. The microscope was constructed from a modified web-camera and implemented on a Raspberry Pi computer. Three aspects of microscope control were tested, including single image capture, focus control and time-lapse imaging. The Twitter embodiment enabled users to send ‘tweets’ directly to the microscope. Image data acquired by the microscope was then returned to the user through a Twitter reply and stored permanently on the photo-sharing platform Flickr, along with any relevant metadata. Local control of the microscope was also implemented by utilizing the video game Minecraft, in situations where Internet connectivity is not present or stable. A virtual laboratory was constructed inside the Minecraft world and player actions inside the laboratory were linked to specific microscope functions. Here, we present the methodology and results of these experiments and discuss possible limitations and future extensions of this work.

A Technique to Determine Unsteady-State Inhibition Kinetics in the Activated Sludge Process

1989 ◽  
Vol 21 (6-7) ◽  
pp. 593-602 ◽  
Author(s):  
Andrew T. Watkin ◽  
W. Wesley Eckenfelder
Keyword(s):  
Activated Sludge ◽  
Kinetic Parameters ◽  
Curve Fitting ◽  
Glucose Utilization ◽  
Batch Reactor ◽  
Synthetic Data ◽  
Utilization Rate ◽  
Fitting Algorithm ◽  
Test Reactor ◽  
Two Parameter

A technique for rapidly determining Monod and inhibition kinetic parameters in activated sludge is evaluated. The method studied is known as the fed-batch reactor technique and requires approximately three hours to complete. The technique allows for a gradual build-up of substrate in the test reactor by introducing the substrate at a feed rate greater than the maximum substrate utilization rate. Both inhibitory and non-inhibitory substrate responses are modeled using a nonlinear numerical curve-fitting technique. The responses of both glucose and 2,4-dichlorophenol (DCP) are studied using activated sludges with various acclimation histories. Statistically different inhibition constants, KI, for DCP inhibition of glucose utilization were found for the various sludges studied. The curve-fitting algorithm was verified in its ability to accurately retrieve two kinetic parameters from synthetic data generated by superimposing normally distributed random error onto the two parameter numerical solution generated by the algorithm.

Fast Transaction-Level Model for Direct Memory Access Controller

2019 ◽  
Vol 28 (04) ◽  
pp. 1950059
Author(s):  
Mona Safar ◽  
Magdy A. El-Moursy ◽  
Ahmed Tarek ◽  
Ahmed Emad ◽  
Ahmed Hesham ◽  
...  
Keyword(s):  
Open Source ◽  
Direct Memory Access ◽  
System Level ◽  
The Past ◽  
Simulation Speed ◽  
Proposed Model ◽  
Level Model ◽  
Data Bus ◽  
Transaction Level ◽  
Simulation Time

Transaction-Level Modeling (TLM) has been widely used in system-level design in the past few years. Simulation speed of Virtual Platforms (VPs) depends mainly on the transactions which are initiated by the Programmer’s View (PV) models of the VP devices. PV models are required to run at highest simulation speed. Data bus width as a hardware (HW) parameter should not reduce simulation speed of the modeled transactions. Furthermore, HW-related parameters should only be accounted for when considering timing of the models. A fast SystemC-TLM model is developed for the widely used ARM PrimeCell PL080 DMAC IP. The performance of the proposed model is validated against a developed RTL model for the same device. The effect of the transactions granularity on simulation speed is determined. Different programmed transfers are simulated and compared with open-source Quick Emulator (QEMU)-based models. The developed model is compared with the developed RTL, the open-source QEMU model, and the existing ARM Fast Model (AFM). It is shown that simulation time of the developed model is reduced by two orders of magnitude as compared to the other existing models.

Seasonal deposition of phytodetritus to the deep-sea floor

1986 ◽  
Vol 88 ◽  
pp. 265-279 ◽  
Author(s):  
A. L. Rice ◽  
D. S. M. Billett ◽  
J. Fry ◽  
A. W. G. John ◽  
R. S. Lampitt ◽  
...  
Keyword(s):  
Deep Sea ◽  
Benthic Communities ◽  
Time Lapse ◽  
Sediment Traps ◽  
Temporal Variations ◽  
Sea Floor ◽  
Porcupine Seabight ◽  
The Past ◽  
Sea Bed ◽  
Seasonal Deposition

SynopsisEvidence has accumulated over the past twenty years to suggest that the deep-sea environment is not as constant as was at one time thought, but exhibits temporal variations related to the seasonally in the overlying surface waters. Recent results from deep-moored sediment traps suggest that this coupling is mediated through the sedimentation of organic material, while observations in the Porcupine Seabight indicate that in this region, at least, there is a major and rapid seasonal deposition of aggregated phytodetritus to the sea-floor at slope and abyssal depths.This paper summarises the results of the Porcupine Seabight studies over the past five years or so, using time-lapse sea-bed photography and microscopic, microbiological and chemical analyses of samples of phytodetritus and of the underlying sediment. The data are to some extent equivocal, but they suggest that the seasonal deposition is a regular and dramatic phenomenon and that the material undergoes relatively little degradation during its passage through the water column. The mechanisms leading to the aggregation of the phytodetritus have not been identified, and it is not yet known whether the phenomenon is geographically widespread nor whether it is of significance to the deep-living mid-water and benthic communities.

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