Automating your Daily Image Analysis Tasks with Amira Software
Instructor
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Jan Giesebrecht
Thermo Fisher Scientific
Germany
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Brief Bio
After a decade of image processing work and lecturing medical students at the largest university clinic in Europe – the Charité Berlin – Dr. Giesebrecht joined Thermo Fisher Scientific addressing all kinds of image analysis problems in the Life Sciences and Materials Science.
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Abstract
Powerful image processing tools are essential to the modern researcher's workflow. Thermo Scientific Amira Software now comes with a new mechanism to store and execute proven image data processing workflows for massive image data sets. During this tutorial, you will learn how Amira Software can automate and speed up your image analysis when dealing with many data sets from the same origin and with the same analytical question. The workflow creation process will be explained and demonstrated using a life science dataset, including steps such as image filtering, segmentation, or the extraction of user-defined statistics from the data. Recipes can be easily shared with your peers, and form an easy-to-use foundation for your routine image analysis tasks.
Instructions
Registration for Bioimaging 2019 is necessary to attend this tutorial.
For a better experience, we advise attendees to bring their own PC with suitable 3D graphics board for tutorial participation. Check hardware recommendations
Temporary licenses will be provided. To do so, please fill in this form.
This information will be e-mailed to you approx. 1 week before the tutorial date.
Keywords
Amira software, 3D segmentation, image analysis, image processing, automation
Aims and Learning Objectives
Introduction to automation of image processing and analysis
Target Audience
Anyone performing image processing
Prerequisite Knowledge of Audience
None
Detailed Outline
Introduction to the basics of Amira Software and its new data processing automation tools
Simulations of Cell Flow in Microchannels with Object-in-fluid Module in open-source ESPResSo Software Package
Instructor
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Ivan Cimrak
University of Zilina, Faculty of Management Science and Informatics
Slovak Republic
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Brief Bio
After his PhD and a post-doc studies in numerical mathematics at Ghent University, Belgium, Dr. Cimrak focused his research interests on cell flow modelling. He founded a Cell-in-fluid Biomedical Modelling and Computations group at University of Zilina, with currently more than 10 members. His research topics are since then all aspects of biomechanical cell modelling, biomedical image and video data processing, and machine learning algorithms in biomedical image processing.
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Abstract
Laboratory experiments involving flow of cells inside microchannels have been used in many research areas involving cell separation, rare cell isolation, tumour cell capture, various types of cell manipulation, etc. Computational modelling and even more specifically, the computer implementation of these models, allow to simulate processes inside such microfluidic devices and to tackle frontiers of the state-of-the-art microfluidic platforms. We have developed a module Object-in-fluid within the open-source scientific package ESPResSo that enables simulation of individual cells with their specific elastic properties. Object-in-fluid is based on the coupled lattice Boltzmann - immersed boundary method, fully resolving the mechanics of the cells and their interactions with blood plasma. These models help predict the transport of cells in microfluidic flows. In this tutorial we learn basics of cell mechanics and the development of underlying models. We will create simple scripts and we will have hands-on session with the module Object-in-fluid.
Keywords
blood cell modelling, simulations, fluid flow
Aims and Learning Objectives
Learn the basics of blood flow modelling
Learn basics of Object-in-fluid software module
Create simple cell flow simulations
Target Audience
Biologists with the desire to use computational models
Computer scientists with interest in cell modelling
Reserachers interested in or with expertise in blood flow modelling
Experimentalists working in microfluidics
Prerequisite Knowledge of Audience
No special knowledge is required. Notebooks with installed software will be available.
Detailed Outline
The tutorial will consist of two parts:
Part 1 - Talk (20min):
Short introduction to cell modelling
Some specifics of the red blood cell model used in Object-in-fluid module
Part 2 - Hands-on session using the computers (70min):
Intro to the scripting language python
Intro to the visualization of the results
Commented walk-through of a sample script simulating a simple experiment
Extending of the script with more features
From Offline towards Real-Time: a Wearable HAR System Using Biosensors Integrated into a Knee Bandage
Instructor
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Hui Liu
University of Bremen
Germany
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Abstract
During this tutorial, we will introduce a framework for the acquisition, processing and application of biosignals recorded from biosensors integrated into a knee bandage. Such a framework involves the appropriate equipment in devices and sensors, the long-term recording and archiving of corresponding multi-sensory biosignal data, the semi-automatic annotation and segmentation of these data, and the HAR (Human Activity Recognition). You will understand not only how to build an offline HAR system, but also how to realize a real-time HAR system based on the offline foundation. Plenty of topics relating to the real-time HAR will be covered in this tutorial, including the experimental tuning of system parameters which balances recognition accuracy with real-time performance, the intuitive visualization of biosignals as well as n-best recognition results in the graphical user interfaces, and the on-the-air extensions for rapid prototyping of applications.
Keywords
Human Activity Recognition, Biodevices, Biosensors, Biosignals, Wearable Devices, Rehabilitation Technology, Signal Processing
Aims and Learning Objectives
Introduction to realization of offline and real-time wearable HAR systems using biosensors integrated into a knee bandage
Target Audience
Students and Researchers who study or have interest on wearable HAR
Prerequisite Knowledge of Audience
None
Detailed Outline
Hardware: Devices and Sensors; Software: Recording, Segmentation and Annotation; Multi-channel Biosignal Processing; Offline Wearable HAR System: Modeling, Tuning, Training, Decoding and Evaluation; Realization and topics of Real-time Wearable HAR System.
A Guided Exploration through Signal Acquisition and Processing with biosignalsplux and biosignalsnotebooks
Instructor
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Guilherme Ramos
Plux Wireless Biosignals
Portugal
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Brief Bio
Guilherme Ramos is Research Software Engineer in PLUX - Wireless Biosignals, a Portuguese technological company specially dedicated in developing systems for acquiring and processing physiological signals. He has a master’s degree in Biomedical Engineering from the Faculty of Sciences and Technology of NOVA University of Lisbon. Between July and December of 2018, he dedicated his time to research, working as a collaborator of Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), developing more practical knowledge about physiological signal acquisition and processing, one of the scientific areas with greater interest and expectations for him, together with Machine Learning functionalities, concepts and the future impact of new discoveries in this topic. Since January of 2019 he assumed his functions as a Research Software Engineer at PLUX, continuing the instructive partnership started during the execution of master thesis research.
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Abstract
A researcher is the explorer of the present, trying constantly to discover new paths to previously unachievable scientific enigmas. However, this journey does not need to be done alone! With biosignalsnotebooks, Plux want to extend the experience of its clients, describing, with a step-by-step tutorials, how some signal processing tasks can be easily applicable to the physiological signals collected with the Plux acquisition systems (in a first stage focused on biosignalsplux).
Keywords
biosignalsplux;biosignalsnotebooks;OpenSignals;signal acquisition;signal processing;biosignals.
Aims and Learning Objectives
A demo of biosignalsnotebooks learning tool will be done in BIOSTEC Conference having as main purposes the presentation and dissemination of the project (with an explanation of how to access these resources, the current available notebooks and the future perspectives), collect a direct feedback of the researchers about some topics that can be explored in future notebooks (taking into consideration the needs of current or potential clients), awareness of the potential clients that biosignalsnotebooks functionalities are always dependent of an hardware component for acquiring the signals that will be processed (which can be a good opportunity to explain the advantages and capabilities of biosignalsplux).
With the previously established bridge between biosignalsnotebooks and biosignalsplux, some other resources can be presented, like the sensor datasheets and the new Signal Samples (together with a demonstration of biosignalsplux usage).
Learning Objectives:
- How to quickly get ready to use biosignalsplux;
- Access and usage of the main OpenSignals functionalities;
- Understanding of some processing tasks described on biosignalsnotebooks.
Target Audience
-Researchers;
-Participants interested in technological applications;
-Participants concerned about physiological signal processing tasks.
Prerequisite Knowledge of Audience
There are none relevant prerequisites for audience.
However a basic knowledge about signal processing can be important (but not essential) to the audience understand better the presentation topics.
Detailed Outline
[Intro]
1.Start with the presentation of some physiological signals that can be studied;
[Hardware]
1.Explain that the previous described physiological signals can be easily acquired with biosignalsplux (Plux acquisition system);
2.Present the device capabilities and the list of available sensors;
[Software]
1.Explanation of how the biosignalsplux acquired signals can reach the computer (through OpenSignals software);
2.Demonstration of the steps that should be followed in order to a signal acquisition can be successfully done (from hardware configuration to signal processing);
3.How to extend biosignalsplux/OpenSignals experience with biosignalsnotebooks;
4.Answering the question "What is biosignalsnotebooks?";
5.A walk through the biosignalsnotebooks learning resources (signal processing tutorials) and the related project websites;
[Conclusions]
Final presentation conclusions and beginning of the trial period for audience explore biosignalsplux, OpenSignals and biosignalsnotebooks resources.
The use of low-cost physiological toolkits in education with a focus on
BITalino (r)evolution
Instructor
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Daniel Osório
Plux
Portugal
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Brief Bio
Daniel Osório is a PhD student in Biomedical Engineering from Faculty of Sciences and Technology of NOVA University of Lisbon. He has a master’s degree in Biomedical Engineering from the Faculty of Sciences and Technology of the University of Coimbra. Between May 2016 and April of 2017, he dedicated his time to research, working as a collaborator of Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), developing more practical knowledge about physiological signal acquisition and processing, focusing his research on electromyography, electrocardiography and posturography. From April 2017 he enrolled in a PhD at FCT-UNL in the field of off-the-person ECG acquisition, in collaboration with PLUX - Wireless Biosignals, a Portuguese technological company specially dedicated in developing solutions for acquiring and processing physiological signals.
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Abstract
Education practical lab has been using several DIY toolkits for education and practical projects in the recent past. With this demo, we present BITalino (r)evolution, one of the most use standard DIY kits in biomedical engineering courses, and showcase several uses cases for signal acquisition in introductory research, teaching signal processing and the development of software that responds with biosignals for biofeedback or other human-computer interaction purposes.
Keywords
Biosignals, BITalino, DIY
Aims and Learning Objectives
The main purpose of this tutorial is to present and disseminate the BITalino kit, by providing examples of its application in universities around the world, academic work where BITalino was used as a data acquisition device, and other projects where BITalino was used as a human-computer interface or in biofeedback.
We are also looking for feedback on how to improve our product.
Target Audience
- Researchers
- Participants interested in biosignals and low-cost signal acquisition platforms.
Prerequisite Knowledge of Audience
None, although some coding and signal processing experience would be interesting to better understand some of the examples.
Detailed Outline
- Overview of PLUX
- Presentation of the BITalino platform
- Examples where BITalino is used
- Signal acquisition in teaching labs
- Signal acquisition in research
- Signal acquisition in biofeedback and HCI
- Demos
- Connecting to BITalino
- Signal acquisition and some basic introduction to biosignals
- Other examples