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Meier R, Hartop E, Pylatiuk C, Srivathsan A. Towards holistic insect monitoring: species discovery, description, identification and traits for all insects. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230120. [PMID: 38705187 PMCID: PMC11070263 DOI: 10.1098/rstb.2023.0120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/25/2024] [Indexed: 05/07/2024] Open
Abstract
Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Rudolf Meier
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Emily Hartop
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
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2
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Brydegaard M, Pedales RD, Feng V, Yamoa ASD, Kouakou B, Månefjord H, Wührl L, Pylatiuk C, Amorim DDS, Meier R. Towards global insect biomonitoring with frugal methods. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230103. [PMID: 38705174 PMCID: PMC11070255 DOI: 10.1098/rstb.2023.0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 05/07/2024] Open
Abstract
None of the global targets for protecting nature are currently met, although humanity is critically dependent on biodiversity. A significant issue is the lack of data for most biodiverse regions of the planet where the use of frugal methods for biomonitoring would be particularly important because the available funding for monitoring is insufficient, especially in low-income countries. We here discuss how three approaches to insect biomonitoring (computer vision, lidar, DNA sequences) could be made more frugal and urge that all biomonitoring techniques should be evaluated for global suitability before becoming the default in high-income countries. This requires that techniques popular in high-income countries should undergo a phase of 'innovation through simplification' before they are implemented more broadly. We predict that techniques that acquire raw data at low cost and are suitable for analysis with AI (e.g. images, lidar-signals) will be particularly suitable for global biomonitoring, while techniques that rely heavily on patented technologies may be less promising (e.g. DNA sequences). We conclude the opinion piece by pointing out that the widespread use of AI for data analysis will require a global strategy for providing the necessary computational resources and training. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Mikkel Brydegaard
- Dept. Physics, Lund University, Sölvegatan 14c, 22362 Lund, Sweden
- Dept. Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden
- Norsk Elektro Optikk, Østensjøveien 34, 0667 Oslo, Norge
- FaunaPhotonics, Støberi Støberigade 14, 2450 København, Denmark
| | - Ronniel D. Pedales
- Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines 1101
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Vivian Feng
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Assoumou saint-doria Yamoa
- Instrumentation, Imaging and Spectroscopy Laboratory, Felix Houphouet-Boigny Institute, BP1093 Yamoussoukro, Ivory Coast
| | - Benoit Kouakou
- Instrumentation, Imaging and Spectroscopy Laboratory, Felix Houphouet-Boigny Institute, BP1093 Yamoussoukro, Ivory Coast
| | - Hampus Månefjord
- Dept. Physics, Lund University, Sölvegatan 14c, 22362 Lund, Sweden
| | - Lorenz Wührl
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Dalton de Souza Amorim
- Departamento de Biologia, FFCLRP, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
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3
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Hayot G, Marcato D, Cramer von Clausbruch CA, Pace G, Strähle U, Colbourne JK, Pylatiuk C, Peravali R, Weiss C, Scholz S, Dickmeis T. Evaluating Toxicity of Chemicals using a Zebrafish Vibration Startle Response Screening System. J Vis Exp 2024. [PMID: 38284527 DOI: 10.3791/66153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024] Open
Abstract
We developed a simple screening system for the evaluation of neuromuscular and general toxicity in zebrafish embryos. The modular system consists of electrodynamic transducers above which tissue culture dishes with embryos can be placed. Multiple such loudspeaker-tissue culture dish pairs can be combined. Vibrational stimuli generated by the electrodynamic transducers induce a characteristic startle and escape response in the embryos. A belt-driven linear drive sequentially positions a camera above each loudspeaker to record the movement of the embryos. In this way, alterations to the startle response due to lethality or neuromuscular toxicity of chemical compounds can be visualized and quantified. We present an example of the workflow for chemical compound screening using this system, including the preparation of embryos and treatment solutions, operation of the recording system, and data analysis to calculate benchmark concentration values of compounds active in the assay. The modular assembly based on commercially available simple components makes this system both economical and flexibly adaptable to the needs of particular laboratory setups and screening purposes.
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Affiliation(s)
- Gaëlle Hayot
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology - Campus Nord
| | - Daniel Marcato
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology - Campus Nord; DITABIS AG - Digital Biomedical Imaging Systems AG
| | | | - Giuseppina Pace
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology - Campus Nord
| | - Uwe Strähle
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology - Campus Nord; Centre for Organismal Studies, Heidelberg University
| | | | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology - Campus Nord
| | - Ravindra Peravali
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology - Campus Nord
| | - Carsten Weiss
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology - Campus Nord
| | - Stefan Scholz
- Department of Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research - UFZ
| | - Thomas Dickmeis
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology - Campus Nord;
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Wang Y, Kanagaraj NK, Pylatiuk C, Mikut R, Peravali R, Reischl M. High-Throughput Data Acquisition Platform for Multi-Larvae Touch-Response Behavior Screening of Zebrafish*. IEEE Robot Autom Lett 2022. [DOI: 10.1109/lra.2021.3134281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Schutera M, Rettenberger L, Pylatiuk C, Reischl M. Methods for the frugal labeler: Multi-class semantic segmentation on heterogeneous labels. PLoS One 2022; 17:e0263656. [PMID: 35134081 PMCID: PMC8824336 DOI: 10.1371/journal.pone.0263656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
Deep learning increasingly accelerates biomedical research, deploying neural networks for multiple tasks, such as image classification, object detection, and semantic segmentation. However, neural networks are commonly trained supervised on large-scale, labeled datasets. These prerequisites raise issues in biomedical image recognition, as datasets are generally small-scale, challenging to obtain, expensive to label, and frequently heterogeneously labeled. Furthermore, heterogeneous labels are a challenge for supervised methods. If not all classes are labeled for an individual sample, supervised deep learning approaches can only learn on a subset of the dataset with common labels for each individual sample; consequently, biomedical image recognition engineers need to be frugal concerning their label and ground truth requirements. This paper discusses the effects of frugal labeling and proposes to train neural networks for multi-class semantic segmentation on heterogeneously labeled data based on a novel objective function. The objective function combines a class asymmetric loss with the Dice loss. The approach is demonstrated for training on the sparse ground truth of a heterogeneous labeled dataset, training within a transfer learning setting, and the use-case of merging multiple heterogeneously labeled datasets. For this purpose, a biomedical small-scale, multi-class semantic segmentation dataset is utilized. The heartSeg dataset is based on the medaka fish’s position as a cardiac model system. Automating image recognition and semantic segmentation enables high-throughput experiments and is essential for biomedical research. Our approach and analysis show competitive results in supervised training regimes and encourage frugal labeling within biomedical image recognition.
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Affiliation(s)
- Mark Schutera
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Baden-Württemberg, Germany
- * E-mail:
| | - Luca Rettenberger
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Baden-Württemberg, Germany
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Baden-Württemberg, Germany
| | - Markus Reischl
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Baden-Württemberg, Germany
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Wührl L, Pylatiuk C, Giersch M, Lapp F, von Rintelen T, Balke M, Schmidt S, Cerretti P, Meier R. DiversityScanner: Robotic handling of small invertebrates with machine learning methods. Mol Ecol Resour 2021; 22:1626-1638. [PMID: 34863029 DOI: 10.1111/1755-0998.13567] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/20/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023]
Abstract
Invertebrate biodiversity remains poorly understood although it comprises much of the terrestrial animal biomass, most species and supplies many ecosystem services. The main obstacle is specimen-rich samples obtained with quantitative sampling techniques (e.g., Malaise trapping). Traditional sorting requires manual handling, while molecular techniques based on metabarcoding lose the association between individual specimens and sequences and thus struggle with obtaining precise abundance information. Here we present a sorting robot that prepares specimens from bulk samples for barcoding. It detects, images and measures individual specimens from a sample and then moves them into the wells of a 96-well microplate. We show that the images can be used to train convolutional neural networks (CNNs) that are capable of assigning the specimens to 14 insect taxa (usually families) that are particularly common in Malaise trap samples. The average assignment precision for all taxa is 91.4% (75%-100%). This ability of the robot to identify common taxa then allows for taxon-specific subsampling, because the robot can be instructed to only pick a prespecified number of specimens for abundant taxa. To obtain biomass information, the images are also used to measure specimen length and estimate body volume. We outline how the DiversityScanner can be a key component for tackling and monitoring invertebrate diversity by combining molecular and morphological tools: the images generated by the robot become training images for machine learning once they are labelled with taxonomic information from DNA barcodes. We suggest that a combination of automation, machine learning and DNA barcoding has the potential to tackle invertebrate diversity at an unprecedented scale.
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Affiliation(s)
- Lorenz Wührl
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Matthias Giersch
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Florian Lapp
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Michael Balke
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | - Stefan Schmidt
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | - Pierfilippo Cerretti
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
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López-Olmeda JF, Zhao H, Reischl M, Pylatiuk C, Lucon-Xiccato T, Loosli F, Foulkes NS. Long photoperiod impairs learning in male but not female medaka. iScience 2021; 24:102784. [PMID: 34308290 PMCID: PMC8283132 DOI: 10.1016/j.isci.2021.102784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/12/2021] [Accepted: 06/23/2021] [Indexed: 01/01/2023] Open
Abstract
Day length in conjunction with seasonal cycles affects many aspects of animal biology. We have studied photoperiod-dependent alterations of complex behavior in the teleost, medaka (Oryzias latipes), a photoperiodic breeder, in a learning paradigm whereby fish have to activate a sensor to obtain a food reward. Medaka were tested under a long (14:10 LD) and short (10:14 LD) photoperiod in three different groups: mixed-sex, all-males, and all-females. Under long photoperiod, medaka mixed-sex groups learned rapidly with a stable response. Unexpectedly, males-only groups showed a strong learning deficit, whereas females-only groups performed efficiently. In mixed-sex groups, female individuals drove group learning, whereas males apparently prioritized mating over feeding behavior resulting in strongly reduced learning performance. Under short photoperiod, where medaka do not mate, male performance improved to a level similar to that of females. Thus, photoperiod has sex-specific effects on the learning performance of a seasonal vertebrate.
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Affiliation(s)
- Jose Fernando López-Olmeda
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain
| | - Haiyu Zhao
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- School of Life Sciences, Lanzhou University, No.222 South Tianshui Road, 730000 Lanzhou, PR China
| | - Markus Reischl
- Institute for Applied Computer Science, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christian Pylatiuk
- Institute for Applied Computer Science, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Tyrone Lucon-Xiccato
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Felix Loosli
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Nicholas S. Foulkes
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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Petani L, Koker L, Herrmann J, Hagenmeyer V, Gengenbach U, Pylatiuk C. Recent Developments in Ozone Sensor Technology for Medical Applications. Micromachines (Basel) 2020; 11:mi11060624. [PMID: 32604832 PMCID: PMC7344528 DOI: 10.3390/mi11060624] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/10/2020] [Accepted: 06/24/2020] [Indexed: 11/25/2022]
Abstract
There is increasing interest in the utilisation of medical gases, such as ozone, for the treatment of herniated disks, peripheral artery diseases, and chronic wounds, and for dentistry. Currently, the in situ measurement of the dissolved ozone concentration during the medical procedures in human bodily liquids and tissues is not possible. Further research is necessary to enable the integration of ozone sensors in medical and bioanalytical devices. In the present review, we report selected recent developments in ozone sensor technology (2016–2020). The sensors are subdivided into ozone gas sensors and dissolved ozone sensors. The focus thereby lies upon amperometric and impedimetric as well as optical measurement methods. The progress made in various areas—such as measurement temperature, measurement range, response time, and recovery time—is presented. As inkjet-printing is a new promising technology for embedding sensors in medical and bioanalytical devices, the present review includes a brief overview of the current approaches of inkjet-printed ozone sensors.
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9
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Schutera M, Just S, Gierten J, Mikut R, Reischl M, Pylatiuk C. Machine Learning Methods for Automated Quantification of Ventricular Dimensions. Zebrafish 2019; 16:542-545. [PMID: 31536467 DOI: 10.1089/zeb.2019.1754] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Medaka (Oryzias latipes) and zebrafish (Danio rerio) contribute substantially to our understanding of the genetic and molecular etiology of human cardiovascular diseases. In this context, the quantification of important cardiac functional parameters is fundamental. We have developed a framework that segments the ventricle of a medaka hatchling from image sequences and subsequently quantifies ventricular dimensions.
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Affiliation(s)
- Mark Schutera
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
| | - Steffen Just
- Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Jakob Gierten
- Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany.,Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Ralf Mikut
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
| | - Markus Reischl
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
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Pylatiuk C, Zhao H, Gursky E, Reischl M, Peravali R, Foulkes N, Loosli F. DIY Automated Feeding and Motion Recording System for the Analysis of Fish Behavior. SLAS Technol 2019; 24:394-398. [PMID: 31013465 DOI: 10.1177/2472630319841412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fish species such as medaka or zebrafish are widely used as animal models to study physiology, disease development, and treatment efficacy. They are also used to study the rapidly growing field of behavior research, such as social interactions, anxiety, and the influence of environmental factors. Here we describe an automated experimental setup allowing the recording of general locomotor activity in combination with a food-on-demand system. It can simply be built with some basic electronic knowledge. Our setup enables the recording of locomotor and feeding activity of several fish for long-term studies, excluding disturbing external influences. A description of the automated recording system is given, as well as examples of recordings to illustrate its applicability for the study of fish behavior. The construction manual and operation instructions can be downloaded for free.
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Affiliation(s)
- Christian Pylatiuk
- 1 Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Haiyu Zhao
- 2 Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Eduard Gursky
- 2 Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Markus Reischl
- 1 Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Ravindra Peravali
- 2 Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Nicholas Foulkes
- 2 Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Felix Loosli
- 2 Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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Neukum A, Bartschat A, Breitwieser H, Strähle U, Dickmeis T, Pylatiuk C. Automated Classification of Fertilized Zebrafish Embryos. Zebrafish 2019; 16:326-328. [PMID: 30939078 DOI: 10.1089/zeb.2019.1728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Alexander Neukum
- 1 Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
| | - Andreas Bartschat
- 1 Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
| | - Helmut Breitwieser
- 1 Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
| | - Uwe Strähle
- 2 Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
| | - Thomas Dickmeis
- 2 Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
| | - Christian Pylatiuk
- 1 Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Eggenstein, Germany
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12
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Pott A, Shahid M, Köhler D, Pylatiuk C, Weinmann K, Just S, Rottbauer W. Therapeutic Chemical Screen Identifies Phosphatase Inhibitors to Reconstitute PKB Phosphorylation and Cardiac Contractility in ILK-Deficient Zebrafish. Biomolecules 2018; 8:biom8040153. [PMID: 30463267 PMCID: PMC6315389 DOI: 10.3390/biom8040153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022] Open
Abstract
Patients with inherited dilated cardiomyopathy (DCM) often suffer from severe heart failure based on impaired cardiac contractility leading to increased morbidity and mortality. Integrin-linked kinase (ILK) as a part of the cardiac mechanical stretch sensor was found to be an essential genetic regulator of cardiac contractility. Integrin-linked kinase localizes to z-disks and costameres in vertebrate hearts and regulates the activity of the signaling molecule protein kinase B (PKB/Akt) by controlling its phosphorylation. Despite identification of several potential drug targets in the ILK signaling pathway, pharmacological treatment strategies to restore contractile function in ILK-dependent cardiomyopathies have not been established yet. In recent years, the zebrafish has emerged as a valuable experimental system to model human cardiomyopathies as well as a powerful tool for the straightforward high-throughput in vivo small compound screening of therapeutically active substances. Using the ILK deficient zebrafish heart failure mutant main squeeze (msq), which shows reduced PKB phosphorylation and thereby impaired cardiac contractile force, we identified here, in an automated small compound screen, the protein phosphatase inhibitors calyculin A and okadaic acid significantly restoring myocardial contractile function by reconstituting PKB phosphorylation in msq ILK-deficient zebrafish embryos.
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Affiliation(s)
- Alexander Pott
- Department of Internal Medicine II, Ulm University, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Maryam Shahid
- Department of Internal Medicine II, Ulm University, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Doreen Köhler
- Department of Internal Medicine III, University of Heidelberg, D-69120 Heidelberg, Germany.
| | - Christian Pylatiuk
- Institute of Applied Computer Science, Karlsruhe Institute of Technology, D-76344 Eggenstein-Leopoldshafen, Germany.
| | - Karolina Weinmann
- Department of Internal Medicine II, Ulm University, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Steffen Just
- Department of Internal Medicine II, Ulm University, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
| | - Wolfgang Rottbauer
- Department of Internal Medicine II, Ulm University, Albert-Einstein-Allee 23, D-89081 Ulm, Germany.
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Abstract
A versatile robot platform is presented that can be used to design low-cost custom made microscopes in do-ityourself construction. All components like the framework, the linear drives, robot controller and driver, the illumination and the camera are described as well as optional features like fluorescence microscopy and auto-focus. Finally, an application for automated imaging of 3D-cell cultures in 96-well microplates is presented.
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14
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Bedell V, Buglo E, Marcato D, Pylatiuk C, Mikut R, Stegmaier J, Scudder W, Wray M, Züchner S, Strähle U, Peravali R, Dallman JE. Zebrafish: A Pharmacogenetic Model for Anesthesia. Methods Enzymol 2018; 602:189-209. [PMID: 29588029 PMCID: PMC10559369 DOI: 10.1016/bs.mie.2018.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
General anesthetics are small molecules that interact with and effect the function of many different proteins to promote loss of consciousness, amnesia, and sometimes, analgesia. Owing to the complexity of this state transition and the transient nature of these drug/protein interactions, anesthetics can be difficult to study. The zebrafish is an emerging model for the discovery of both new genes required for the response to and side effects of anesthesia. Here we discuss the tools available to manipulate the zebrafish genome, including both genetic screens and genome engineering approaches. Additionally, there are various robust behavior assays available to study anesthetic and other drug responses. These assays are available for single-gene study or high throughput for genetic or drug discovery. Finally, we present a case study of using propofol as an anesthetic in the zebrafish. These techniques and protocols make the zebrafish a powerful model to study anesthetic mechanisms and drug discovery.
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Affiliation(s)
- Victoria Bedell
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.
| | - Elena Buglo
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States; Dr. John T. MacDonald Foundation, University of Miami, Miami, FL, United States; University of Miami, Coral Gables, FL, United States
| | - Daniel Marcato
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Christian Pylatiuk
- Institute of Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ralf Mikut
- Institute of Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Johannes Stegmaier
- Institute of Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Will Scudder
- University of Miami, Coral Gables, FL, United States
| | - Maxwell Wray
- University of Miami, Coral Gables, FL, United States
| | - Stephan Züchner
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States; Dr. John T. MacDonald Foundation, University of Miami, Miami, FL, United States
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ravindra Peravali
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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15
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Gierten J, Loosli F, Gehrig J, Pylatiuk C, Fitzgerald T, Birney E, Wittbrodt J, Gorenflo M. Systems Genetics Approach to Study Congenital Heart Disease in a Fish Model. Thorac Cardiovasc Surg 2018. [DOI: 10.1055/s-0038-1628326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- J. Gierten
- Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - F. Loosli
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Eggenstein-Leopoldshafen, Germany
| | - J. Gehrig
- ACQUIFER is a division of DITABIS, Digital Biomedical Imaging Systems AG, Pforzheim, Germany
| | - C. Pylatiuk
- Karlsruhe Institute of Technology (KIT), Institute for Applied Computer Science (IAI), Eggenstein-Leopoldshafen, Germany
| | - T. Fitzgerald
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - E. Birney
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - J. Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - M. Gorenflo
- Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
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16
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Breitwieser H, Dickmeis T, Vogt M, Ferg M, Pylatiuk C. Fully Automated Pipetting Sorting System for Different Morphological Phenotypes of Zebrafish Embryos. SLAS Technol 2017; 23:128-133. [PMID: 29220613 DOI: 10.1177/2472630317745780] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Systems biology methods, such as transcriptomics and metabolomics, require large numbers of small model organisms, such as zebrafish embryos. Manual separation of mutant embryos from wild-type embryos is a tedious and time-consuming task that is prone to errors, especially if there are variable phenotypes of a mutant. Here we describe a zebrafish embryo sorting system with two cameras and image processing based on template-matching algorithms. In order to evaluate the system, zebrafish rx3 mutants that lack eyes due to a patterning defect in brain development were separated from their wild-type siblings. These mutants show glucocorticoid deficiency due to pituitary defects and serve as a model for human secondary adrenal insufficiencies. We show that the variable phenotypes of the mutant embryos can be safely distinguished from phenotypic wild-type zebrafish embryos and sorted from one petri dish into another petri dish or into a 96-well microtiter plate. On average, classification of a zebrafish embryo takes approximately 1 s, with a sensitivity and specificity of 87% to 95%, respectively. Other morphological phenotypes may be classified and sorted using similar techniques.
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Affiliation(s)
- Helmut Breitwieser
- 1 Institute for Applied Computer Science, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas Dickmeis
- 2 Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Marcel Vogt
- 1 Institute for Applied Computer Science, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Marco Ferg
- 2 Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Christian Pylatiuk
- 1 Institute for Applied Computer Science, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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17
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Armbruster P, Oster Y, Vogt M, Pylatiuk C. Design of a mechanism for converting the energy of knee motions by using electroactive polymers. ACTA ACUST UNITED AC 2017; 62:643-652. [PMID: 28258972 DOI: 10.1515/bmt-2016-0138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 01/19/2017] [Indexed: 11/15/2022]
Abstract
Harvesting energy from human body motions has become a promising option to prolong battery life for powering medical devices for autonomy. Up to now, different generating principles including dielectric electroactive polymers (DEAPs) have been suggested for energy conversion. However, there is a lack of mechanisms that are specifically designed to convert energy with DEAPs. In a proof of concept study, a mechanical system was designed for stretching DEAPs in those phases of the gait cycle, in which the muscles mainly perform negative work. Rotational movements of the knee joint are transformed into linear movements by using a cable pull. The DEAP can be charged during the stretching phase and discharged during releasing and allows for the conversion of kinetic energy into electric energy. To evaluate the concept, tests were conducted. It was found that the developed body energy harvesting (BEH) system has a performance in the range of 24-40 μW at normal walking speed. The converted energy is sufficient for powering sensors in medical devices such as active orthoses or prostheses.
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18
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Abstract
AbstractConverting energy from human upper limb motions into electrical energy is a challenge, as low frequency movements have to be converted into repetitive movements to effectively drive electromechanical generators. The prototype of an electromagnetic linear generator with gyrating mass is presented. The mechanical motion model first was simulated and the design was evaluated during different activities. An average power output of about 50 μW was determined with a maximum power output of 2.2 mW that is sufficient to operate sensors for health monitoring.
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Affiliation(s)
- Stephan Brunner
- Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Maximilian Gerst
- Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Christian Pylatiuk
- Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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19
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Schutera M, Dickmeis T, Mione M, Peravali R, Marcato D, Reischl M, Mikut R, Pylatiuk C. Automated phenotype pattern recognition of zebrafish for high-throughput screening. Bioengineered 2017; 7:261-5. [PMID: 27285638 DOI: 10.1080/21655979.2016.1197710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Over the last years, the zebrafish (Danio rerio) has become a key model organism in genetic and chemical screenings. A growing number of experiments and an expanding interest in zebrafish research makes it increasingly essential to automatize the distribution of embryos and larvae into standard microtiter plates or other sample holders for screening, often according to phenotypical features. Until now, such sorting processes have been carried out by manually handling the larvae and manual feature detection. Here, a prototype platform for image acquisition together with a classification software is presented. Zebrafish embryos and larvae and their features such as pigmentation are detected automatically from the image. Zebrafish of 4 different phenotypes can be classified through pattern recognition at 72 h post fertilization (hpf), allowing the software to classify an embryo into 2 distinct phenotypic classes: wild-type versus variant. The zebrafish phenotypes are classified with an accuracy of 79-99% without any user interaction. A description of the prototype platform and of the algorithms for image processing and pattern recognition is presented.
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Affiliation(s)
- Mark Schutera
- a Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen , Germany
| | - Thomas Dickmeis
- b Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen , Germany
| | - Marina Mione
- b Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen , Germany
| | - Ravindra Peravali
- b Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen , Germany
| | - Daniel Marcato
- b Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen , Germany
| | - Markus Reischl
- a Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen , Germany
| | - Ralf Mikut
- a Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen , Germany
| | - Christian Pylatiuk
- a Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen , Germany
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20
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Steimer KC, Zimmermann C, Zeilfelder J, Pylatiuk C, Stork W. Portable auricular device for real-time swallow and chew detection. Current Directions in Biomedical Engineering 2016. [DOI: 10.1515/cdbme-2016-0031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Monitoring a person’s nutritional consumption is costly and complex. To solve this problem a new technique is proposed to draw conclusions of a person’s food intake. The air pressure signal, recorded in the external acoustic meatus, is used to detect swallow and chew events. A portable device has been developed to record this pressure signal. Due to the constraint of running on a low-power microcontroller, real-time algorithms, used in pattern and speech recognition, were used to develop methods to automatically detect swallow and chew events. A binary classifier was trained by means of manually annotated data sets. Direct comparisons with state of the art technology and tests with several subjects are provided for evaluation purposes.
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Affiliation(s)
- Konrad C. Steimer
- Forschungszentrum Informatik (FZI), Haid-und-Neu-Straße 10-14, 76131 Karlsruhe, GER
| | - Christoph Zimmermann
- Forschungszentrum Informatik (FZI) and KIT, Institute for Applied Computer Science (IAI), 76131 Karlsruhe, GER
| | - Jennifer Zeilfelder
- Forschungszentrum Informatik (FZI) and KIT, Institute for Applied Computer Science (IAI), 76131 Karlsruhe, GER
| | - Christian Pylatiuk
- Forschungszentrum Informatik (FZI) and KIT, Institute for Applied Computer Science (IAI), 76131 Karlsruhe, GER
| | - Wilhelm Stork
- Forschungszentrum Informatik (FZI) and KIT, Institute for Applied Computer Science (IAI), 76131 Karlsruhe, GER
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21
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Marcato D, Alshut R, Breitwieser H, Mikut R, Strahle U, Pylatiuk C, Peravali R. An automated and high-throughput Photomotor Response platform for chemical screens. Annu Int Conf IEEE Eng Med Biol Soc 2016; 2015:7728-31. [PMID: 26738083 DOI: 10.1109/embc.2015.7320183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The zebrafish (Danio rerio) is a well-established vertebrate model organism. Its embryos are used extensively in biology and medicine to perform chemical screens to identify drug candidates or to evaluate teratogenicity and embryotoxicity of substances. Behavioral readouts are increasingly used to assess the effects of compounds on the nervous system. Early stage zebrafish show characteristic behavioral features at stages between 30 and 42 hours post fertilization (hpf) when exposed to a short and bright light flash. This so-called Photomotor Response (PMR) is a reaction of the nervous system of the fish and can be used as a marker in screenings for neuroactive chemicals. To probe a broad and diverse chemical space, many different substances have to be tested and repeated observations are necessary to warrant statistical significance of the results. Although PMR-based chemical screens must use a large number of specimens, there is no sophisticated, automated high-throughput platform available which ensures minimal human intervention. Here we report a PMR platform that was developed by combining an improved automatic sample handling with a remotely controllable microscope setup and an image analysis pipeline. Using infrared illumination during automatic sample preparation, we were able to eliminate excess amounts of visible light that could potentially alter the response results. A remotely controlled microscope setup allows us to screen entire 96-well microtiter plates without human presence that could disturb the embryos. The development of custom video analysis software, including single egg detection, enables us to detect variance among treated specimens and extract easy to interpret numerical values representing the PMR motion. By testing several neuroactive compounds we validated the workflow that can be used to analyze more than one thousand zebrafish eggs on a single 96-well plate.
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22
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Pylatiuk C, Sanchez D, Mikut R, Alshut R, Reischl M, Hirth S, Rottbauer W, Just S. Automatic zebrafish heartbeat detection and analysis for zebrafish embryos. Zebrafish 2014; 11:379-83. [PMID: 25003305 DOI: 10.1089/zeb.2014.1002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A fully automatic detection and analysis method of heartbeats in videos of nonfixed and nonanesthetized zebrafish embryos is presented. This method reduces the manual workload and time needed for preparation and imaging of the zebrafish embryos, as well as for evaluating heartbeat parameters such as frequency, beat-to-beat intervals, and arrhythmicity. The method is validated by a comparison of the results from automatic and manual detection of the heart rates of wild-type zebrafish embryos 36-120 h postfertilization and of embryonic hearts with bradycardia and pauses in the cardiac contraction.
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Affiliation(s)
- Christian Pylatiuk
- 1 Institute for Applied Computer Science (IAI) , Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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23
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Pylatiuk C, Metzger F, Wiegand R, Bretthauer G. Kinetic energy scavenging in a prosthetic foot using a fluidic system. BIOMED ENG-BIOMED TE 2013; 58:353-8. [PMID: 23912217 DOI: 10.1515/bmt-2012-0092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 07/15/2013] [Indexed: 11/15/2022]
Abstract
The use of active prostheses for the lower extremity is limited by the amount of electric energy stored in batteries. A promising way to extend their usage time is to convert motions generated by the human body during walking to electrical energy. A first functioning prototype was designed to transfer kinetic energy from heel contact and forefoot contact to a generator by using a fluidic system. Experimental results show that walking with the system generates an average electrical power of 0.8 W. The design of the energy scavenging system (ESS) is presented and results are discussed.
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Affiliation(s)
- Christian Pylatiuk
- Institute for Applied Computer Science IAI, Karlsruhe Institute of Technology KIT, Germany.
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24
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Pfriem A, Pylatiuk C, Alshut R, Ziegener B, Schulz S, Bretthauer G. A modular, low-cost robot for zebrafish handling. Annu Int Conf IEEE Eng Med Biol Soc 2013; 2012:980-3. [PMID: 23366058 DOI: 10.1109/embc.2012.6346097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The zebrafish (danio rerio) is one of the most important model organisms in modern drug discovery and disease modeling. Handling and analyzing large numbers of zebrafish larvae require an immense manpower and involve time-consuming manual processes. A novel modular, robotic platform for high-throughput screening is being developed at BioRobotLab (KIT). In this article the fish sorter, which is a robotic device for the automation of a manual process in bio analysis, is presented. The fish sorter detects randomly spread zebrafish eggs and larvae up to an age of 120 hours post fertilization (hpf) in Petri dishes and transfers them to standard 96- or 384- well plates. The robot is controlled by an advanced algorithm with sensor-based process control. Fast and precise hardware components lead to a high working speed and success rate >= 95%.
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Affiliation(s)
- Alexander Pfriem
- Institute of Applied Computer Science, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
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25
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Spomer W, Pfriem A, Alshut R, Just S, Pylatiuk C. High-throughput screening of zebrafish embryos using automated heart detection and imaging. ACTA ACUST UNITED AC 2012; 17:435-42. [PMID: 23053930 DOI: 10.1177/2211068212464223] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Over the past decade, the zebrafish has become a key model organism in genetic screenings and drug discovery. A number of genes have been identified to affect the development of the shape and functioning of the heart, leading to zebrafish mutants with heart defects. The development of semiautomated microscopy systems has allowed for the investigation of drugs that reverse a disease phenotype on a larger scale. However, there is a lack of automated feature detection, and commercially available computer-aided microscopes are expensive. Screening of the zebrafish heart for drug discovery typically includes the identification of heart parameters, such as the frequency or fractional shortening. Until now, screening processes have been characterized by manual handling of the larvae and manual microscopy. Here, an intelligent robotic microscope is presented, which automatically identifies the orientation of a zebrafish in a micro well. A predefined region of interest, such as the heart, is detected automatically, and a video with higher magnification is recorded. Screening of a 96-well plate takes 35 to 55 min, depending on the length of the videos. Of the zebrafish hearts, 75% are recorded accurately without any user interaction. A description of the system, including the graphical user interface, is given.
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Affiliation(s)
- Waldemar Spomer
- Institute for Applied Computer Science, KIT-Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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26
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Schill O, Wiegand R, Schmitz B, Matthies R, Eck U, Pylatiuk C, Reischl M, Schulz S, Rupp R. OrthoJacket: an active FES-hybrid orthosis for the paralysed upper extremity. ACTA ACUST UNITED AC 2011; 56:35-44. [PMID: 21210758 DOI: 10.1515/bmt.2010.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The loss of the grasp function in cervical spinal cord injured (SCI) patients leads to life-long dependency on caregivers and to a tremendous decrease of the quality of life. This article introduces the novel non-invasive modular hybrid neuro-orthosis OrthoJacket for the restoration of the restricted or completely lost hand and arm functions in high tetraplegic SCI individuals. The primary goal of the wearable orthosis is to improve the paralysed upper extremity function and, thus, to enhance a patient's independence in activities of daily living. The system combines the advantage of orthotics in mechanically stabilising joints together with the possibilities of functional electrical stimulation for activation of paralysed muscles. In patients with limited capacity, for force generation, flexible fluidic actuators are used to support the movement. Thus, the system is not only intended for functional restoration but also for training. Several sensor systems together with an intelligent signal processing allow for automatic adaptation to the anatomical and neurological individualities of SCI patients. The integration of novel user interfaces based on residual muscle activities and detection of movement intentions by real-time data mining methods will enable the user to autonomously control the system in a natural and cooperative way.
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Affiliation(s)
- Oliver Schill
- Karlsruhe Institute of Technology, Institute of Applied Computer Science and Automation, Germany.
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27
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Abstract
Normative data of the grip force distribution necessary to complete functional tasks are limited. Small force sensors have been specially designed for accurate measurement of the dynamic handgrip force distribution by attaching them to the palmar surface of the hand. Seventeen healthy participants performed three different tasks, each requiring a different functional prehension pattern. When cylindrical objects were manipulated, the highest average grip forces were found at the fingertips and the thumb, followed by the middle finger. In a spherical grasp pattern, the contributions by the thumb, ring and small fingers always exceeded 71% of the total grip force. The highest local forces of 9.9 N were measured when a zip was closed with a tip pinch. Individual finger forces were found to differ by gender, but not by hand dimension and age. The results are useful for biomechanical modelling of the hand, for designing ergonomic tool grips, and for evaluating hand function.
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Affiliation(s)
- C Pylatiuk
- Institute for Applied Computer Science, Forschungszentrum Karlsruhe GmbH, PO Box 3640, D-76021, Karlsruhe, Germany.
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28
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Bretthauer G, Schulz S, Pylatiuk C, Beck S, Reischl M. [A new adaptive hand prosthesis]. HANDCHIR MIKROCHIR P 2008; 40:40-5. [PMID: 18283617 DOI: 10.1055/s-2007-989427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
In the paper, a new adaptive hand prosthesis developed in the Institute of Applied Computer Sciences of the Forschungszentrum Karlsruhe is described. Starting from the state-of-the-art, the requirements of the hand prosthesis are derived and the realisation of the new prosthesis is shown. Finally the results obtained are discussed.
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Affiliation(s)
- G Bretthauer
- Forschungszentrum Karlsruhe, Institut für Angewandte Informatik, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen.
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29
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Abstract
The results of a survey of 54 persons with upper limb amputations who anonymously completed a questionnaire on an Internet homepage are presented. The survey ran for four years and the participants were divided into groups of females, males, and children. It was found that the most individuals employ their myoelectric hand prosthesis for 8 hours or more. However, the survey also revealed a high level of dissatisfaction with the weight and the grasping speed of the devices. Activities for which prostheses should be useful were stated to include handicrafts, personal hygiene, using cutlery, operation of electronic and domestic devices, and dressing/undressing. Moreover, additional functions, e.g., a force feedback system, independent movements of the thumb, the index finger, and the wrist, and a better glove material are priorities that were identified by the users as being important improvements the users would like to see in myoelectric prostheses.
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Affiliation(s)
- Christian Pylatiuk
- Forschungszentrum Karlsruhe, Institute for Applied Computer Science, Karlsruhe, Germany.
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30
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Pylatiuk C, Mounier S, Kargov A, Schulz S, Bretthauer G. Progress in the development of a multifunctional hand prosthesis. Conf Proc IEEE Eng Med Biol Soc 2007; 2004:4260-3. [PMID: 17271245 DOI: 10.1109/iembs.2004.1404187] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A new experimental hand prosthesis design is presented that differs from that of conventional prostheses. With the objective of addressing consumers' requirements, functionality was increased and cosmetic appearance became more natural. By integrating a hydraulic system with 8 small fluidic actuators at the digit joints, different important grasping patterns of everyday life can be performed. These are: power grasp, hook grasp, precision grasp, lateral pinch, and a posture to operate a keyboard with the extended index. As a result of multi-articulation and the inherent compliancy of the actuators, objects can be grasped adaptively. Moreover, a vibrotactile feedback system makes the prosthesis controllable without visual attention. For a more natural appearance, the hand is covered by a cosmetic silicone rubber glove. The hands are designed for performing activities of everyday life, including office work. The new hand design can help closing the gap between purely cosmetic hands and functional hands.
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Affiliation(s)
- C Pylatiuk
- Institute of Applied Computer Science, Forschungszentrum Karlsruhe GmbH, Germany
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31
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Abstract
BACKGROUND A new generation of arm prostheses is being developed worldwide. These so-called bionic prostheses are intended to offer additional functions, such as sensory feedback, extended range of possible movement, intuitive movement control as far as possible, and a more natural cosmetic appearance. STATE OF THE ART IN RESEARCH AND DEVELOPMENT In recent years, prosthetic components with much enhanced performance have been developed for use at various levels of the upper limb. Artificial hands that allow for additional grips are are being tested in clinical settings. Innovative methods of signal acquisition and communication with the patient are being intensively researched. CONCLUSION Several patients have been provided with prototypes of new arm prostheses. At the moment, the results are limited by the restricted communication between patient and prosthesis. However, we can expect the options for prosthesis control to be extended in the near future.
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Affiliation(s)
- C Pylatiuk
- Institut für Angewandte Informatik, Forschungszentrum Karlsruhe GmbH, Hermann von Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen,
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32
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Pylatiuk C, Kargov A, Schulz S. Interphalangeal joint moments in functional grasping. J Biomech 2006. [DOI: 10.1016/s0021-9290(06)85062-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
PURPOSE Consumers want new prosthetic hand designs that have increased functionality, better cosmetic appearance, and lower weight. METHODS New lightweight hands that fulfill these demands can be designed by integrating a hydraulic system with small fluidic actuators at the digit joints. RESULTS Two different designs of lightweight experimental prosthetic hand are presented. The weight of the first hand is reduced by 50% compared to a conventional prosthetic hand, whereas the functionality of the second hand is increased by additional prehension types. Optionally, a tactile feedback system can be integrated. Due to multiple articulated digits and flexible materials, both hands are able to conform to the shape of an object held. This significantly reduces the necessary grip force and results in stable holding of an object. For a natural appearance, the hands are covered with a cosmetic silicone rubber glove.
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Affiliation(s)
- Christian Pylatiuk
- Institute for Applied Computer Sciences (IAI), Forschungszentrum Karlsruhe, Karlsruhe, Germany.
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Abstract
PURPOSE The aim of this study is to analyse the grip force distribution for different prosthetic hand designs and the human hand fulfilling a functional task. METHOD A cylindrical object is held with a power grasp and the contact forces are measured at 20 defined positions. The distributions of contact forces in standard electric prostheses, in a experimental prosthesis with an adaptive grasp, and in human hands as a reference are analysed and compared. Additionally, the joint torques are calculated and compared. RESULTS Contact forces of up to 24.7 N are applied by the middle and distal phalanges of the index finger, middle finger, and thumb of standard prosthetic hands, whereas forces of up to 3.8 N are measured for human hands. The maximum contact forces measured in a prosthetic hand with an adaptive grasp are 4.7 N. The joint torques of human hands and the adaptive prosthesis are comparable. CONCLUSIONS The analysis of grip force distribution is proposed as an additional parameter to rate the performance of different prosthetic hand designs.
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Affiliation(s)
- Artem Kargov
- Institute for Applied Computer Science (IAI), Forschungszentrum Karlsruhe GmbH, Eggenstein-Leopoldshafen, Germany.
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35
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Abstract
Raising control possibilities of myoelectric prostheses--The control of hand prostheses is based on the surface scan of myoelectric voltage caused by muscle contractions in an amputees arm stump. So far available prostheses only perform up to two different grip types. This paper introduces a control scheme that is able to execute a variety of grip types dependent on the patient's control signals. Therefore a platform is presented to adapt control parameters especially to the patients anatomy. Developed algorithms are flashed on a microcontroller, processing data online and controlling a new generation of prostheses (FZK-prosthesis, Forschungszentrum Karlsruhe).
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Affiliation(s)
- M Reischl
- Institut für Angewandte Informatik (IAI), Forschungszentrum Karlsruhe GmbH, Deutschland.
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Fritz C, Braune HJ, Pylatiuk C, Pohl M. Silent period following transcranial magnetic stimulation: a study of intra- and inter-examiner reliability. Electroencephalogr Clin Neurophysiol 1997; 105:235-40. [PMID: 9216492 DOI: 10.1016/s0924-980x(97)96675-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Transcranial magnetic stimulation-evoked silent period (SP) has been attributed largely to the activity of intracortical inhibitory systems and recent reports provided evidence that it is a useful indicator of central motor disturbances. We studied the intra- and inter-examiner reliability of SP measurements in 28 healthy subjects. In 15 subjects SP measurements were performed by one single examiner and repeated by the same examiner 3 days and 7 days later, showing a high degree of intra-examiner reliability over time. In another subgroup consisting of 13 volunteers SP measurements were performed on the same subject by three different examiners, demonstrating a higher level of variability. In both subgroups we found a high interindividual variability ranging from 44-258 ms and a considerably lower side-to-side difference within subjects. Our results suggest that longitudinal assessments of the SP in patients with central motor involvement should optimally be performed by a single examiner. Regarding the wide range of possible SP durations in healthy subjects the intraindividual side-to-side symmetry seems to be the most valuable parameter.
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Affiliation(s)
- C Fritz
- Department of Neurology, Philipps-University Marburg, Germany
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