FPM app: an open-source application for simple and intuitive Fourier ptychographic reconstruction

Fourier ptychographic microscopy (FPM) is a computational microscopy technique that enables large field of view and high-resolution microscopic imaging of biological samples. However, the FPM does not yet have an adequately capable open-source software. In order to fill this gap we are presenting novel, simple, universal, semi-automatic and highly intuitive graphical user interface (GUI) open-source application called the FPM app enabling wide-scale robust FPM reconstruction. Apart from implementing the FPM in accessible GUI app, we also made several improvements in the FPM image reconstruction process itself, making the FPM more automatic, noise-robust and faster.

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X-Light: an open-source software written in Python to determine the residual stress by X-ray diffraction

Journal of Applied Crystallography ◽

10.1107/s160057672100618x ◽

2021 ◽

Vol 54 (4) ◽

Author(s):

Tu-Quoc-Sang Pham ◽

Guillaume Geandier ◽

Nicolas Ratel-Ramond ◽

Charles Mareau ◽

Benoit Malard

Keyword(s):

Residual Stress ◽

User Interface ◽

Synchrotron Radiation ◽

Stress Analysis ◽

Open Source ◽

Graphical User Interface ◽

Open Source Software ◽

Diffraction Data ◽

X Ray Diffraction ◽

X Ray

X-Light is an open-source software that is written in Python with a graphical user interface. X-Light was developed to determine residual stress by X-ray diffraction. This software can process the 0D, 1D and 2D diffraction data obtained with laboratory diffractometers or synchrotron radiation. X-Light provides several options for stress analysis and five functions to fit a peak: Gauss, Lorentz, Pearson VII, pseudo-Voigt and Voigt. The residual stress is determined by the conventional sin2ψ method and the fundamental method.

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Miniscope-LFOV: A large field of view, single cell resolution, miniature microscope for wired and wire-free imaging of neural dynamics in freely behaving animals

10.1101/2021.11.21.469394 ◽

2021 ◽

Author(s):

Changliang Guo ◽

Garrett J. Blair ◽

Megha Sehgal ◽

Federico N. Sangiuliano Jimka ◽

Arash Bellafard ◽

...

Keyword(s):

Single Cell ◽

Open Source ◽

Coaxial Cable ◽

Field Of View ◽

Large Field ◽

Head Orientation ◽

Cranial Window ◽

Multiple Imaging ◽

Free Data ◽

Freely Behaving

We present a large field of view (FOV) open-source miniature microscope (MiniLFOV) designed to extend the capabilities of the UCLA Miniscope platform to large-scale, single cell resolution neural imaging in freely behaving large rodents and head-fixed mice. This system is capable of multiple imaging configurations, including deep brain imaging using implanted optical probes and cortical imaging through cranial windows. The MiniLFOV interfaces with existing open-source UCLA Miniscope DAQ hardware and software, can achieve single cell resolution imaging across a 3.6 × 2.7 mm field of view at 23 frames per second, has an electrically adjustable working distance of up to 3.5 mm±150 µm using an onboard electrowetting lens, incorporates an absolute head-orientation sensor, and weighs under 14 grams. The MiniLFOV provides a 30-fold larger FOV and yields 20-fold better sensitivity than Miniscope V3, and a 12-fold larger FOV with 2-fold better sensitivity than Miniscope V4. Power and data transmission are handled through a single, flexible coaxial cable down to 0.3 mm in diameter facilitating naturalistic behavior. We validated the MiniLFOV in freely behaving rats by simultaneously imaging >1000 GCaMP7s expressing neurons in the CA1 layer of the hippocampus and in head-fixed mice by simultaneously imaging ~2000 neurons in the mouse dorsal cortex through a 4 × 4 mm cranial window. For freely behaving experiments, the MiniLFOV supports optional wire-free operation using a 3.5 g wire-free data acquisition expansion board which enables close to 1-hour of wire-free recording with a 400 mAh (7.5 g) on-board single-cell lithium-polymer battery and expands wire-free imaging techniques to larger animal models. We expect this new open-source implementation of the UCLA Miniscope platform will enable researchers to address novel hypotheses concerning brain function in freely behaving animals.

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Onboard catalogue of known X-ray sources for SVOM/ECLAIRs

Astronomy and Astrophysics ◽

10.1051/0004-6361/202038995 ◽

2020 ◽

Vol 645 ◽

pp. A18 ◽

Cited By ~ 1

Author(s):

N. Dagoneau ◽

S. Schanne ◽

J. Rodriguez ◽

J.-L. Atteia ◽

B. Cordier

Keyword(s):

Energy Band ◽

Gamma Ray ◽

Background Level ◽

High Energy ◽

Low Noise ◽

Field Of View ◽

Large Field ◽

Galactic Centre ◽

Reconstruction Process ◽

X Ray

The SVOM mission currently under development will carry various instruments, and in particular the coded-mask telescope ECLAIRs, with a large field of view of about 2 sr, operating in the 4–150 keV energy band. The main goal of ECLAIRs is to detect high-energy transients such as gamma-ray bursts. Its onboard trigger software will search for new hard X-ray sources appearing in the sky, as well as peculiar behaviour (e.g. strong outbursts) from known sources, in order to repoint the satellite to perform follow-up observations with its onboard narrow-field-of-view instruments. The presence of known X-ray sources must be disentangled from the appearance of new sources. This is done with the help of an onboard source catalogue, which we present in this paper. As an input we use catalogues of X-ray sources detected by Swift/BAT and MAXI/GSC and we study the influence of the sources on ECLAIRs’ background level and on the quality of the sky-image reconstruction process. We show that the influence of the sources depends on the pointing direction on the sky, on the energy band, and on the exposure time. In the Galactic centre, the contribution from known sources largely dominates the cosmic X-ray background, which is, on the contrary, the main background in sky regions lacking strong sources. We also demonstrate the need to clean the contributions of these sources in order to maintain a low noise level in the sky images and to maintain a low threshold for the detection of new sources without introducing false triggers. We briefly describe one of our cleaning methods and its challenges. Finally, we present the overall structure of the onboard catalogue and the way it will be used to perform the source cleaning and disentangle detections of new sources from outbursts of known sources.

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SIMON: open-source knowledge discovery platform

10.1101/2020.08.16.252767 ◽

2020 ◽

Author(s):

Adriana Tomic ◽

Ivan Tomic ◽

Levi Waldron ◽

Ludwig Geistlinger ◽

Max Kuhn ◽

...

Keyword(s):

Machine Learning ◽

Knowledge Discovery ◽

Open Source ◽

Graphical User Interface ◽

Open Source Software ◽

State Of The Art ◽

Machine Learning Algorithms ◽

High Dimensional ◽

Biomedical Data ◽

Programming Skills

AbstractData analysis and knowledge discovery has become more and more important in biology and medicine with the increasing complexity of the biological datasets, but necessarily sophisticated programming skills and in-depth understanding of algorithms needed pose barriers to most biologists and clinicians to perform such research. We have developed a modular open-source software SIMON to facilitate the application of 180+ state-of-the-art machine learning algorithms to high-dimensional biomedical data. With an easy to use graphical user interface, standardized pipelines, automated approach for machine learning and other statistical analysis methods, SIMON helps to identify optimal algorithms and provides a resource that empowers non-technical and technical researchers to identify crucial patterns in biomedical data.

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Detection of cerebral tauopathy in P301L mice using high-resolution large-field multifocal illumination fluorescence microscopy

10.1101/2020.05.18.101188 ◽

2020 ◽

Author(s):

Ruiqing Ni ◽

Zhenyue Chen ◽

Juan A. Gerez ◽

Gloria Shi ◽

Quanyu Zhou ◽

...

Keyword(s):

High Resolution ◽

Fluorescence Microscopy ◽

Field Of View ◽

Large Field ◽

Depth Of Focus ◽

Microscopy Technique ◽

Microscopy Techniques ◽

Small Field Of View

AbstractCurrent intravital microscopy techniques visualize tauopathy with high-resolution, but have a small field-of-view and depth-of-focus. Herein, we report a transcranial detection of tauopathy over the entire cortex of P301L tauopathy mice using large-field multifocal illumination (LMI) fluorescence microscopy technique and luminescent conjugated oligothiophenes. In vitro assays revealed that fluorescent ligand h-FTAA is optimal for in vivo tau imaging, which was confirmed by observing elevated probe retention in the cortex of P301L mice compared to non-transgenic littermates. Immunohistochemical staining further verified the specificity of h-FTAA to detect tauopathy in P301L mice. The new imaging platform can be leveraged in pre-clinical mechanistic studies of tau spreading and clearance as well as longitudinal monitoring of tau targeting therapeutics.

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Implementation of Obstruction Avoiding Robot using Ultrasonic Sensor and Arduino UNO

International Journal of Recent Technology and Engineering - 2 ◽

10.35940/ijrte.d5295.118419 ◽

2019 ◽

Vol 8 (4) ◽

pp. 7335-7339

Keyword(s):

Open Source ◽

Open Source Software ◽

Online Community ◽

Low Voltage ◽

Ultrasonic Sensor ◽

Field Of View ◽

Community Of Learners ◽

Servo Motor ◽

Arduino Uno ◽

Internal Code

This project attempts to create an obstruction avoiding robot which can automatically sense the presence of an obstruction in its path and avoid them. It intelligently detects barrier present in its path through the ultrasonic sensors, with the help of the internal code from the Arduino UNO, decisions are made to avoid the barriers. This has been achieved by using an ultrasonic sensor and the development board Arduino UNO. The ultrasonic sensor is mounted on a servo motor at the front of the vehicle for a wider field of view. The ultrasonic sensor acquires data which is processed by the Arduino which then decides the direction of travel for the robot. The robot requires low voltage and minimal maintenance for continued operation. Arduino being an open-source software has gained popularity for the creation of basic prototypes due to its relative simplicity in both design and coding. It also boasts of a large online community of learners and engineers.

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