scholarly journals Micro-Magellan: A flexible, open source acquisition software for high throughput biological light microscopy

2016 ◽  
Author(s):  
Henry Pinkard ◽  
Nico Stuurman ◽  
Kaitlin Corbin ◽  
Ronald Vale ◽  
Matthew F Krummel
Keyword(s):  
User Interface ◽  
Light Microscopy ◽  
Open Source ◽  
High Throughput ◽  
Biological Samples ◽  
Abstraction Layer ◽  
Wide Range ◽  
Automated Imaging ◽  
Hardware Abstraction Layer ◽  
High Throughput Imaging

We demonstrate the capabilities of μMagellan: a flexible, open source microscopy software for reproducible high throughput imaging of biological samples across heterogeneous scales of space and time. μMagellan provides a simple user interface for exploration and automated imaging of non-cuboidal regions. By utilizing the hardware abstraction layer of μManager, μMagellan provides a powerful and extensible platform for imaging heterogeneous biological samples on a wide range of existing microscopes.

scholarly journals MULTI-CHANNEL CONTROL SYSTEM FOR IN-SITU LABORATORY LOADING DEVICES

2018 ◽  
Vol 18 ◽  
pp. 15 ◽  
Author(s):  
Václav Rada ◽  
Tomáš Fíla ◽  
Petr Zlámal ◽  
Daniel Kytýř ◽  
Petr Koudelka
Keyword(s):  
Open Source ◽  
Software Tool ◽  
Cnc Machine ◽  
Control Software ◽  
Wide Range ◽  
Hardware Abstraction Layer ◽  
Channel Control ◽  
Python Programming ◽  
Loading Devices

In recent years, open-source applications have replaced proprietary software in many fields. Especially open-source software tools based on Linux operating system have wide range of utilization. In terms of CNC solutions, an open-source system LinuxCNC can be used. However, the LinuxCNC control software and the graphical user interface (GUI) could be developed only on top of Hardware Abstraction Layer. Nevertheless, the LinuxCNC community provided Python Interface, which allows for controlling CNC machine using Python programming language, therefore whole control software can be developed in Python. The paper focuses on a development of a multi-process control software mainly for in-house developed loading devices operated at our institute. The software tool is based on the LinuxCNC Python Interface and Qt framework, which gives the software an ability to be modular and effectively adapted for various devices.

A mixed real-time robot hardware abstraction layer (R-HAL)

2018 ◽  
Vol 02 (01) ◽  
pp. 1850010 ◽  
Author(s):  
Giuseppe F. Rigano ◽  
Luca Muratore ◽  
Arturo Laurenzi ◽  
Enrico M. Hoffman ◽  
Nikos G. Tsagarakis
Keyword(s):  
Upper Body ◽  
Control Software ◽  
Software Developers ◽  
Know How ◽  
Abstraction Layer ◽  
Wide Range ◽  
Application Programming ◽  
Hardware Abstraction Layer ◽  
Robotic Platforms ◽  
And Control

The rapid advances in robotics have recently led to the developments of a wide range of robotic platforms that exhibit significant differences at the hardware components level. Consequently, this poses a significant challenge to robot software developers since they have to know how every hardware device in the robot works to ensure their software’s compatibility when transferring/reusing their code on different robots. In this paper we present a new Robot Hardware Abstraction Layer (R-HAL) that permits to seamlessly program and control any robotic platform powered by the XBot control software framework. The implementation details of the R-HAL are introduced. The R-HAL is extensively validated through simulation trials and experiments with a wide range of dissimilar robotic platforms, among them the COMAN and WALK-MAN humanoids, the KUKA LWR and the CENTAURO upper body. The results attained demonstrate in practice the gained benefits in terms of code compatibility, reuse and portability, and finally unified application programming even for robots with significantly diverse hardware.

Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night

2018 ◽  
Vol 16 (01) ◽  
pp. 1740011 ◽  
Author(s):  
Olga Kiseleva ◽  
Ekaterina Poverennaya ◽  
Alexander Shargunov ◽  
Andrey Lisitsa
Keyword(s):  
User Interface ◽  
Open Source ◽  
High Throughput ◽  
Graphical User Interface ◽  
Modern Science ◽  
Human Proteome ◽  
Tandem Ms ◽  
Report Generation ◽  
Manual Search ◽  
Human Proteins

Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data. Nowadays, the routine manual search does not satisfy the “speed” of modern science any longer. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. We compared the contribution of each of the eight search engines (X!Tandem, MS-GF[Formula: see text], MS Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an open-source graphical user interface SearchGUI ( http://searchgui.googlecode.com ) into total result of proteoforms identification and optimized set of engines working simultaneously. We also compared the results of our search combination with Mascot results using protein kit UPS2, containing 48 human proteins. We selected combination of X!Tandem, MS-GF[Formula: see text] and OMMSA as the most time-efficient and productive combination of search. We added homemade java-script to automatize pipeline from file picking to report generation. These settings resulted in rise of the efficiency of our customized pipeline unobtainable by manual scouting: the analysis of 192 files searched against human proteome (42153 entries) downloaded from UniProt took 11[Formula: see text]h.

Automated imaging MS: Toward high throughput imaging mass spectrometry

2010 ◽  
Vol 73 (6) ◽  
pp. 1279-1282 ◽  
Author(s):  
Liam A. McDonnell ◽  
Alexandra van Remoortere ◽  
René J.M. van Zeijl ◽  
Hans Dalebout ◽  
Marco R. Bladergroen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Imaging Mass Spectrometry ◽  
Automated Imaging ◽  
High Throughput Imaging ◽  
Imaging Ms

scholarly journals High-throughput imaging of biological samples with Delmic's FAST-EM

2021 ◽  
Vol 27 (S1) ◽  
pp. 558-560
Author(s):  
Job Fermie ◽  
Wilco Zuidema ◽  
Radim Šejnoha ◽  
Anouk Wolters ◽  
Ben Giepmans ◽  
...  
Keyword(s):  
High Throughput ◽  
Biological Samples ◽  
High Throughput Imaging

scholarly journals SraTailor: GUI software for visualizing high-throughput sequence read archives

2014 ◽  
Author(s):  
Shinya Oki ◽  
Kazumitsu Maehara ◽  
Yasuyuki Ohkawa ◽  
Chikara Meno
Keyword(s):  
User Interface ◽  
Data Processing ◽  
High Throughput ◽  
Graphical User Interface ◽  
Software Package ◽  
Sequence Data ◽  
Command Line ◽  
Accession Number ◽  
Wide Range

Raw high-throughput sequence data are deposited in public databases as SRAs (Sequence Read Archives) and are publically available to every researcher. However, in order to graphically visualize the sequence data of interest, the corresponding SRAs must be downloaded and converted into BigWig format through complicated command-line processing. This task requires users to possess skill with script languages and sequence data processing, a requirement that prevents a wide range of biologists from exploiting SRAs. To address these challenges, we developed SraTailor, a GUI (Graphical User Interface) software package that automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of SraTailor: entering an accession number of an SRA and clicking the mouse are the only steps required in order to obtain BigWig-formatted files and to graphically visualize the extents of reads at given loci. SraTailor is also able to make peak calls and files of other formats, and the software also accepts various command-line-like options. Therefore, this software makes SRAs fully exploitable by a wide range of biologists. SraTailor is freely available at http://www.dev.med.kyushu-u.ac.jp/sra_tailor/.

scholarly journals HiCTMap: Detection and Analysis of Chromosome Territory Structure and Position by High-throughput Imaging

2017 ◽  
Author(s):  
Ziad Jowhar ◽  
Prabhakar Gudla ◽  
Sigal Shachar ◽  
Darawalee Wangsa ◽  
Jill L. Russ ◽  
...  
Keyword(s):  
High Precision ◽  
High Throughput ◽  
Large Population ◽  
Chromosome Territory ◽  
Automated Image Analysis ◽  
Nuclear Space ◽  
Chromosome Territories ◽  
Wide Range ◽  
High Throughput Imaging ◽  
2D And 3D

AbstractThe spatial organization of chromosomes in the nuclear space is an extensively studied field that relies on measurements of structural features and 3D positions of chromosomes with high precision and robustness. However, no tools are currently available to image and analyze chromosome territories in a high-throughput format. Here, we have developed High-throughput Chromosome Territory Mapping (HiCTMap), a method for the robust and rapid analysis of 2D and 3D chromosome territory positioning in mammalian cells. HiCTMap is a high-throughput imaging-based chromosome detection method which enables routine analysis of chromosome structure and nuclear position. Using an optimized FISH staining protocol in a 384-well plate format in conjunction with a bespoke automated image analysis workflow, HiCTMap faithfully detects chromosome territories and their position in 2D and 3D in a large population of cells per experimental condition. We apply this novel technique to visualize chromosomes 18, X, and Y in male and female primary human skin fibroblasts, and show accurate detection of the correct number of chromosomes in the respective genotypes. Given the ability to visualize and quantitatively analyze large numbers of nuclei, we use HiCTMap to measure chromosome territory area and volume with high precision and determine the radial position of chromosome territories using either centroid or equidistant-shell analysis. The HiCTMap protocol is also compatible with RNA FISH as demonstrated by simultaneous labeling of X chromosomes and Xist RNA in female cells. We suggest HiCTMap will be a useful tool for routine precision mapping of chromosome territories in a wide range of cell types and tissues.

scholarly journals Protein inference using PIA workflows and PSI standard file formats

2018 ◽  
Author(s):  
Julian Uszkoreit ◽  
Yasset Perez-Riverol ◽  
Britta Eggers ◽  
Katrin Marcus ◽  
Martin Eisenacher
Keyword(s):  
Mass Spectrometry ◽  
Open Source ◽  
High Throughput ◽  
Biological Samples ◽  
Shotgun Proteomics ◽  
Original Sample ◽  
Protein Inference ◽  
File Formats ◽  
Inference Algorithms ◽  
Identification And Quantification

AbstractProteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here, proteins are digested, which leads to the identification and quantification of peptides instead. While often neglected, the important step of protein inference needs to be conducted to infer from the identified peptides to the actual proteins in the original sample.In this work, we highlight some of the previously published and newly added features of the tool PIA – Protein Inference Algorithms, which helps the user with the protein inference of measured samples. We also highlight the importance of the usage of PSI standard file formats, as PIA is the only current software supporting all available standards used for spectrum identification and protein inference. Additionally, we briefly describe the benefits of working with workflow environments for proteomics analyses and show the new features of the PIA nodes for the KNIME Analytics Platform. Finally, we benchmark PIA against a recently published dataset for isoform detection.PIA is open source and available for download on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the community extensions inside the KNIME analytics platform.

scholarly journals SPIM-fluid: open source light-sheet based platform for high-throughput imaging

2015 ◽  
Vol 6 (11) ◽  
pp. 4447 ◽  
Author(s):  
Emilio J. Gualda ◽  
Hugo Pereira ◽  
Tiago Vale ◽  
Marta Falcão Estrada ◽  
Catarina Brito ◽  
...  
Keyword(s):  
Open Source ◽  
High Throughput ◽  
Light Sheet ◽  
High Throughput Imaging
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