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Micropilot: automation of fluorescence microscopy–based imaging for systems biology

Christian Conrad, Annelie Wünsche, Tze Heng Tan, Jutta Bulkescher, Frank Sieckmann, Fatima Verissimo, Arthur Edelstein, Thomas Walter, Urban Liebel, Rainer Pepperkok, Jan Ellenberg
2011 Nature Methods  
Reflection-based autofocus 24 was carried out before each prescan acquisition (zoom 1.0). Communication channel with Micropilot was the Windows registry.  ...  The Matrix Screener provided autofocus, multigrid scanning, and as the communication channel Transmission Control Protocol or Internet Protocol (TCP/IP)-based computer-aided microscopy (CAM), available  ... 
doi:10.1038/nmeth.1558 pmid:21258339 pmcid:PMC3086017 fatcat:dajzz3ptufellbgcazwmgnxzea

Total iron measurement in human serum with a novel smartphone-based assay

Michael Serhan, David Jackemeyer, Mindy Long, Mark Sprowls, Ismael Diez Perez, Wolfgang Maret, Fang Chen, Nongjian Tao, Erica Forzani
2020 IEEE Journal of Translational Engineering in Health and Medicine  
The sensor strip has a vertical flow design and is based on an optimized chemical reaction.  ...  Methods: A novel assay equipped with an accurate, storable, and robust dry sensor strip, as well as a smartphone mount and (iPhone) app is used to measure total iron in human serum.  ...  Your legacy will stay with us for ever.  ... 
doi:10.1109/jtehm.2020.3005308 pmid:32832281 pmcid:PMC7433848 fatcat:bzqkyhnnqnahxkrod7pmzgrnli

OVERVIEW OF DIGITAL FORENSICS ALGORITHMS IN DSLR CAMERAS

E. Aminova, I. Trapeznikov, A. Priorov
2017 The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences  
It is considered that the study focuses on the problem of determination of unique feature of DSLR cameras based on optical subsystem artifacts and sensor noises.  ...  Most research in this area based on the mention that the extraction of unique sensor trace of DSLR camera could be possible on the certain stage of the imaging process into the camera.  ...  and produced us the opportunity to realize our possibilities.  ... 
doi:10.5194/isprs-archives-xlii-2-w4-199-2017 fatcat:3ugmycam7ncglpug5mjx4uri7q

GA-Adaptive Template Matching for Offline Shape Motion Tracking Based on Edge Detection: IAS Estimation from the SURVISHNO 2019 Challenge Video for Machine Diagnostics Purposes

Daga, Garibaldi
2020 Algorithms  
Measurement of the IAS can be used as a source of information of the machine condition per se, or for performing angular resampling through Computed Order Tracking, a practice which is essential to highlight  ...  By repeating the analysis frame after frame and focusing on the angular position of the screw head over time, the proposed algorithm can be used as an effective offline video-tachometer able to estimate  ...  Feature-based methods minimize an error measure based on distances in the feature space, while direct methods minimize an error measure based on direct image information collected from all pixels in the  ... 
doi:10.3390/a13020033 fatcat:3x62ehlynjaynoxiaabic3rgdi

Precision Multiband Photometry with a DSLR Camera

M. Zhang, G. Á. Bakos, K. Penev, Z. Csubry, J. D. Hartman, W. Bhatti, M. de Val-Borro
2016 Publications of the Astronomical Society of the Pacific  
We found that the DSLR achieves a best-case median absolute deviation (MAD) of 4.6 mmag per 180 s exposure when the DSLR color channels are combined, and 1000 stars are measured to better than 10 mmag  ...  We conclude that the Canon 60D is a cheap, lightweight device capable of useful photometry in multiple colors.  ...  Based on our own measurements with this camera we produced the diagram shown in Fig. 3 , describing the layout of the different regions on the chip.  ... 
doi:10.1088/1538-3873/128/961/035001 fatcat:e765yhdfdjblpphpibdpnbqmne

Development of miniaturized fluorimetric device for caffeine determination using a smartphone

Natália da Costa Luchiari, Gabrielen Alves da Silva, César Augusto Marasco Júnior, Paulo Clairmont Feitosa de Lima Gomes
2019 RSC Advances  
This study proposes a miniaturized fluorimetric device to determine caffeine in an energy drink and medicines by digital image using a smartphone.  ...  Intra-and inter-day precision of the methods were evaluated based on the relative standard deviation (% RSD) from the calibration curve performed in triplicate.  ...  information of a target analyte, in place of some high cost instrumental techniques like LC-MS/MS. 7, 8 igital image analysis methods are based on the use of a digital sensor like digital cameras, smartphones  ... 
doi:10.1039/c9ra06220c pmid:35530710 pmcid:PMC9074131 fatcat:icavhedwk5fj7exf6iccx3p7wu

Three-dimensional localization microscopy in live flowing cells

Lucien E. Weiss, Yael Shalev Ezra, Sarah Goldberg, Boris Ferdman, Omer Adir, Avi Schroeder, Onit Alalouf, Yoav Shechtman
2020 Zenodo  
The extraction of 3D positions from subcellular objects of interest is achieved by calibrating the depth-dependent response of the imaging system using fluorescent beads mixed with the sample buffer.  ...  A similar change in the inter-loci distance was observable for cells that were fixed prior to imaging (Figure S3 , Methods).  ...  (C) A histogram of localized positions in the two color channels. (D) A histogram of the inter-channel distance between localizations in each dimension. (E) A histogram of the 3D distance measured.  ... 
doi:10.5281/zenodo.3911511 fatcat:jup6bc2jincxtmfdnack4jz5me

A Tetrahedron-Based Heat Flux Signature for Cortical Thickness Morphometry Analysis [chapter]

Yonghui Fan, Gang Wang, Natasha Lepore, Yalin Wang
2018 Lecture Notes in Computer Science  
Layer for Semantic Segmentation 451 A Framework for Identifying Diabetic Retinopathy Based on Anti-noise Detection and Attention-based Fusion 458 Magnetic Resonance Spectroscopy Quantification using Deep  ...  Multiple Instance Decisions Aggregated CNN 392 Respiratory Motion Modelling using cGANs 398 A deep learning-based method for automated performance evaluation in Transesoesophageal Echocardiography 405  ... 
doi:10.1007/978-3-030-00931-1_48 pmid:30338317 pmcid:PMC6191198 fatcat:dqhvpm5xzrdqhglrfftig3qejq

High-throughput multicolor 3D localization in live cells by depth-encoding imaging flow cytometry [article]

Lucien E Weiss, Yael Shalev Ezra, Sarah E Goldberg, Boris Ferdman, Yoav Shechtman
2019 bioRxiv   pre-print
We demonstrate this approach for measuring fluorescently-labeled DNA in vitro and the chromosomal compaction state in large populations of live cells, collecting thousands of samples each minute.  ...  By exploiting the laminar-flow profile in microfluidics, 3D positions can be extracted from cells or other objects of interest by calibrating the depth-dependent response of the imaging system using fluorescent  ...  A similar change in the inter-loci distance was observable for cells that were fixed prior to imaging ( Figure S3 , Methods).  ... 
doi:10.1101/730101 fatcat:bbbqtdtqzrdyfoapbk36g7oq7u

Application of multispectral imaging in quantitative immunohistochemistry study of breast cancer: a comparative study

Wen-Lou Liu, Lin-Wei Wang, Jia-Mei Chen, Jing-Ping Yuan, Qing-Ming Xiang, Gui-Fang Yang, Ai-Ping Qu, Juan Liu, Yan Li
2015 Tumor Biology  
Multispectral imaging (MSI) based on imaging and spectroscopy, as relatively novel to the field of histopathology, has been used in biomedical multidisciplinary researches.  ...  Additionally, the consistency test results indicated the inter-observer agreement was more robust in MS images for HER2 (inter-class correlation coefficient (ICC)=0.95, r s = 0.94), CK5/6 (ICC = 0.90,  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution  ... 
doi:10.1007/s13277-015-4327-9 pmid:26537585 pmcid:PMC4844643 fatcat:abg2khzddza7zav7vczr44pa4m

Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms [article]

Andres M Cardozo Gizzi, Diego I. Cattoni, Jean-Bernard Fiche, Sergio Espinola, Julian Gurgo, Olivier Messina, Christophe Houbron, Yuki Ogiyama, Giorgio-Lucio Papadopoulos, Giacomo Cavalli, Mounia Lagha, Marcelo Nollmann
2018 bioRxiv   pre-print
This allowed us to unveil the changes in 3D chromatin organization occurring upon transcriptional activation and homologous chromosome un-pairing during the awakening of the zygotic genome in intact Drosophila  ...  However, these methods cannot directly examine the interplay between transcriptional activation and chromosome architecture while maintaining spatial information.  ...  Then, we used image-based cross-correlation of these pre-aligned fiducial barcode images to reach sub-pixel accuracy in the correction vector.  ... 
doi:10.1101/434266 fatcat:tl54iepqofafbkz3xde3kxwa4i

Single-molecule binding experiments on long time scales

Mark P. Elenko, Jack W. Szostak, Antoine M. van Oijen
2010 Review of Scientific Instruments  
Total internal reflection fluorescence microscopy is used to image the binding of labeled ligand to molecules specifically coupled to the surface of an optically transparent flow cell.  ...  Total internal reflection fluorescence microscopy is used to image the binding of labeled ligand to molecules specifically coupled to the surface of an optically transparent flow cell.  ...  An initial estimate of the mean residence time was based on a bulk measurement of the off rate for the labeled ligand ͑0.044 min −1 for class V͒.  ... 
doi:10.1063/1.3473936 pmid:20815611 fatcat:obf3oo5wmrh7dgq5a32hojpmw4

Single-cell systems biology by super-resolution imaging and combinatorial labeling

Eric Lubeck, Long Cai
2012 Nature Methods  
We measured the mRNA levels of 32 genes simultaneously in single S. cerevisiae cells.  ...  However, the number of molecular species that can be measured simultaneously is limited by the spectral separability of fluorophores.  ...  We dedicate this paper to Xiaoliang Sunney Xie on the occasion of his 50 th birthday.  ... 
doi:10.1038/nmeth.2069 pmid:22660740 pmcid:PMC3418883 fatcat:oluhsammoza63iiijktw4i6bxi

Nanometer-accuracy distance measurements between fluorophores at the single-molecule level

Stefan Niekamp, Jongmin Sung, Walter Huynh, Gira Bhabha, Ronald D. Vale, Nico Stuurman
2019 Proceedings of the National Academy of Sciences of the United States of America  
We anticipate that these methods will be useful for high-accuracy distance measurements of single molecules over a wide range of length scales.  ...  Here, we describe methods that utilize information about localization and imaging errors to measure distances between two different color fluorophores with ∼1-nm accuracy at distances >2 nm.  ...  Jonsson for the kinesin plasmids and discussions about the kinesin distance measurements.  ... 
doi:10.1073/pnas.1815826116 pmid:30770448 pmcid:PMC6410877 fatcat:g75onbx5xrh5vfppkweih5undi

TADs are 3D structural units of higher-order chromosome organization in Drosophila

Quentin Szabo, Daniel Jost, Jia-Ming Chang, Diego I. Cattoni, Giorgio L. Papadopoulos, Boyan Bonev, Tom Sexton, Julian Gurgo, Caroline Jacquier, Marcelo Nollmann, Frédéric Bantignies, Giacomo Cavalli
2018 Science Advances  
Single-cell analysis revealed a consistent TAD-based physical compartmentalization of the chromatin fiber, with some degree of heterogeneity in intra-TAD conformations and in cis and trans inter-TAD contact  ...  However, whether TADs are true physical units in each cell nucleus or whether they reflect statistical frequencies of measured interactions within cell populations is unclear.  ...  We first used three-color FISH to measure intra-TAD (probes 2-1) versus inter-TAD (probes 2-3) 3D distances, with probes 1 and 3 being at the exact same genomic distance from probe 2.  ... 
doi:10.1126/sciadv.aar8082 pmid:29503869 pmcid:PMC5829972 fatcat:2u4qwgvy3nh45bhp3vazmhchni
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