scholarly journals Instrbuilder: A Python package for electrical instrument control

2019 ◽  
Vol 4 (36) ◽  
pp. 1172 ◽  
Author(s):  
Lucas Koerner
Keyword(s):  
Instrument Control ◽  
Python Package ◽  
Electrical Instrument

Interfacing of a TEM/STEM System to a Computer

1981 ◽  
Vol 39 ◽  
pp. 250-251
Author(s):  
P. Hagemann
Keyword(s):  
Image Analysis ◽  
Transmission Rate ◽  
Analytical Electron Microscopy ◽  
Signal Beam ◽  
Automated Image Analysis ◽  
Beam Deflection ◽  
External Control ◽  
Computer Input ◽  
Instrument Control ◽  
Data Acquisition And Processing

The use of computers in the analytical electron microscopy today shows three different trends (1) automated image analysis with dedicated computer systems, (2) instrument control by microprocessors and (3) data acquisition and processing e.g. X-ray or EEL Spectroscopy.While image analysis in the T.E.M. usually needs a television chain to get a sequential transmission suitable as computer input, the STEM system already has this necessary facility. For the EM400T-STEM system therefore an interface was developed, that allows external control of the beam deflection in TEM as well as the control of the STEM probe and video signal/beam brightness on the STEM screen.The interface sends and receives analogue signals so that the transmission rate is determined by the convertors in the actual computer periphery.

The IBM-PC in electron microscopy

1996 ◽  
Vol 54 ◽  
pp. 612-613
Author(s):  
James F. Mancuso
Keyword(s):  
Head Start ◽  
Image Acquisition ◽  
Cost Effective ◽  
Financial Applications ◽  
Number Of Factors ◽  
Instrument Control ◽  
The Cost ◽  
Training And Support ◽  
Control Image ◽  
Ibm Pc

IBM PC compatible computers are widely used in microscopy for applications ranging from control to image acquisition and analysis. The choice of IBM-PC based systems over competing computer platforms can be based on technical merit alone or on a number of factors relating to economics, availability of peripherals, management dictum, or simple personal preference.IBM-PC got a strong “head start” by first dominating clerical, document processing and financial applications. The use of these computers spilled into the laboratory where the DOS based IBM-PC replaced mini-computers. Compared to minicomputer, the PC provided a more for cost-effective platform for applications in numerical analysis, engineering and design, instrument control, image acquisition and image processing. In addition, the sitewide use of a common PC platform could reduce the cost of training and support services relative to cases where many different computer platforms were used. This could be especially true for the microscopists who must use computers in both the laboratory and the office.

Plug-in scripts for EFTEM automation

1996 ◽  
Vol 54 ◽  
pp. 546-547
Author(s):  
N. D. Evans ◽  
M. K. Kundmann
Keyword(s):  
Electron Microscopy ◽  
National Laboratory ◽  
Oak Ridge ◽  
Multiple User ◽  
Transmission Electron ◽  
Short Period ◽  
User Facility ◽  
Instrument Control ◽  
And Control ◽  
Research Equipment

Post-column energy-filtered transmission electron microscopy (EFTEM) is inherently challenging as it requires the researcher to setup, align, and control both the microscope and the energy-filter. The software behind an EFTEM system is therefore critical to efficient, day-to-day application of this technique. This is particularly the case in a multiple-user environment such as at the Shared Research Equipment (SHaRE) User Facility at Oak Ridge National Laboratory. Here, visiting researchers, who may oe unfamiliar with the details of EFTEM, need to accomplish as much as possible in a relatively short period of time.We describe here our work in extending the base software of a commercially available EFTEM system in order to automate and streamline particular EFTEM tasks. The EFTEM system used is a Philips CM30 fitted with a Gatan Imaging Filter (GIF). The base software supplied with this system consists primarily of two Macintosh programs and a collection of add-ons (plug-ins) which provide instrument control, imaging, and data analysis facilities needed to perform EFTEM.

A basic introduction to image processing using NIH-Image as a model

1994 ◽  
Vol 52 ◽  
pp. 392-393
Author(s):  
John Mansfield
Keyword(s):  
Image Processing ◽  
Digital Image ◽  
Image Acquisition ◽  
Digital Instrument ◽  
Novice User ◽  
Nih Image ◽  
The Past ◽  
Digital World ◽  
The World ◽  
Instrument Control

Advances in camera technology and digital instrument control have meant that in modern microscopy, the image that was, in the past, typically recorded on a piece of film is now recorded directly into a computer. The transfer of the analog image seen in the microscope to the digitized picture in the computer does not mean, however, that the problems associated with recording images, analyzing them, and preparing them for publication, have all miraculously been solved. The steps involved in the recording an image to film remain largely intact in the digital world. The image is recorded, prepared for measurement in some way, analyzed, and then prepared for presentation.Digital image acquisition schemes are largely the realm of the microscope manufacturers, however, there are also a multitude of “homemade” acquisition systems in microscope laboratories around the world. It is not the mission of this tutorial to deal with the various acquisition systems, but rather to introduce the novice user to rudimentary image processing and measurement.

A Macintosh Interface for the Cameca Camebax-Micro Electron Microprobe

1990 ◽  
Vol 48 (1) ◽  
pp. 438-439
Author(s):  
Carl E. Henderson
Keyword(s):  
Electron Microprobe ◽  
Processing Speed ◽  
Word Processing ◽  
State Of The Art ◽  
Computer Control ◽  
Third Party ◽  
Disk Storage ◽  
The Past ◽  
User Facility ◽  
Instrument Control

Over the past few years it has become apparent in our multi-user facility that the computer system and software supplied in 1985 with our CAMECA CAMEBAX-MICRO electron microprobe analyzer has the greatest potential for improvement and updating of any component of the instrument. While the standard CAMECA software running on a DEC PDP-11/23+ computer under the RSX-11M operating system can perform almost any task required of the instrument, the commands are not always intuitive and can be difficult to remember for the casual user (of which our laboratory has many). Given the widespread and growing use of other microcomputers (such as PC’s and Macintoshes) by users of the microprobe, the PDP has become the “oddball” and has also fallen behind the state-of-the-art in terms of processing speed and disk storage capabilities. Upgrade paths within products available from DEC are considered to be too expensive for the benefits received. After using a Macintosh for other tasks in the laboratory, such as instrument use and billing records, word processing, and graphics display, its unique and “friendly” user interface suggested an easier-to-use system for computer control of the electron microprobe automation. Specifically a Macintosh IIx was chosen for its capacity for third-party add-on cards used in instrument control.

scholarly journals GriSPy: A Python package for fixed-radius nearest neighbors search

2020 ◽  
pp. 100443
Author(s):  
M. Chalela ◽  
E. Sillero ◽  
L. Pereyra ◽  
M.A. Garcia ◽  
J.B. Cabral ◽  
...  
Keyword(s):  
Nearest Neighbors ◽  
Fixed Radius ◽  
Python Package

scholarly journals BiSulfite Bolt: A bisulfite sequencing analysis platform

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Colin Farrell ◽  
Michael Thompson ◽  
Anela Tosevska ◽  
Adewale Oyetunde ◽  
Matteo Pellegrini
Keyword(s):  
Data Aggregation ◽  
Bisulfite Sequencing ◽  
Low Complexity ◽  
Sequencing Analysis ◽  
Command Line ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Analysis Platform ◽  
Python Package ◽  
Bisulfite Sequencing Analysis

Abstract Background Bisulfite sequencing is commonly used to measure DNA methylation. Processing bisulfite sequencing data is often challenging owing to the computational demands of mapping a low-complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis-ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt), a fast and scalable bisulfite sequencing analysis platform. BSBolt performs a pre-alignment sequencing read assessment step to improve efficiency when handling asymmetrical bisulfite sequencing libraries. Findings We evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy. Conclusion BSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a Python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under an MIT license.

scholarly journals SynBiopython: an open-source software library for Synthetic Biology

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Jing Wui Yeoh ◽  
Neil Swainston ◽  
Peter Vegh ◽  
Valentin Zulkower ◽  
Pablo Carbonell ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Open Source ◽  
Open Source Software ◽  
Development Projects ◽  
Software Library ◽  
Current State ◽  
Starting Point ◽  
Common Problems ◽  
Data Tracking ◽  
Python Package

Abstract Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.

scholarly journals Robotic natural-orifice IntraCorporeal anastomosis with Extraction (NICE procedure) for complicated diverticulitis

2021 ◽  
Author(s):  
Eric M. Haas ◽  
Thais Reif de Paula ◽  
Roberto Luna-Saracho ◽  
Melissa Sara Smith ◽  
Jean-Paul J. LeFave
Keyword(s):  
Complicated Diverticulitis ◽  
Intracorporeal Anastomosis ◽  
Natural Orifice ◽  
Abdominal Incision ◽  
Stepwise Approach ◽  
Stapling Device ◽  
Video Recordings ◽  
Conversion Rates ◽  
Technical Modifications ◽  
Instrument Control

Abstract Background Totally intracorporeal surgery for left-sided resection carries numerous potential advantages by avoiding crossing staple lines and eliminating the need for an abdominal incision. For those with complicated diverticulitis, minimally invasive surgery is known to be technically challenging due to inflamed tissue, distorted pelvic anatomy, and obliterated tissue planes, resulting in high conversion rates. We aim to illustrate the stepwise approach and modifications required to successful complete the robotic Natural-orifice IntraCorporeal anastomosis with transrectal specimen Extraction (NICE) procedure in this cohort. Methods Consecutive, elective, unselected patients presenting with complicated diverticulitis defined as fistula, abscess and stricture underwent the NICE procedure over a 24-month period. Demographic and intraoperative data were collected, and video recordings were reviewed and edited on encrypted server. Results A total of 60 patients (50% female) underwent the NICE procedure for complicated diverticulitis with a mean age of 58.9 years and mean BMI of 30.7 kg/m2. The mean operative time was 231.6 min. All cases (100%) were achieved with intracorporeal anastomosis using a circular stapling device. All but one patient (98.3%) had successful transrectal extraction of the specimen. Forty-four (73%) of the specimens required a specimen-thinning maneuver to successfully extract the specimen and there were no conversions. We identified seven key technical modifications and considerations to facilitate successful completion of the procedure which are illustrated, including early release of the disease, mesentery-sparing dissection, dual instrument control of the mesenteric vasculature, release of the rectal reflection, use of NICE back table, specimen-thinning maneuver, and closure of the rectal cuff. Conclusion We present a stepwise approach with key modifications to successfully achieve totally robotic intracorporeal resection for those presenting with complicated diverticulitis. This approach may help overcome the technical challenges and provide a foundation for reproducible results.

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