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Automated Region of interest (ROI) finder based on fluorescent signal of cellular spheroids for image analysis to study cell migration
No full text<h3>Automated Region of interest (ROI) finder based on fluorescent signal of cellular spheroids for image analysis to study cell migration</h3><h3>Context and methodology</h3><p>This repository contains two Fiji macros, that were written in the context of the THIRST project (at TU Wien) for the specific use to analyze the cell migration of green-fluorescent protein (GFP) labeled cells over time in a spheroid doublet fusion experiment. The THIRST project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant agreement No. 772464). The Fiji macros were used for data analysis, for the following publication: "Scaffolded spheroids as building blocks for bottom-up cartilage tissue engineering show enhanced bioassembly dynamics" by O.Kopinski-Grünwald and O.Guillaume et al. (2023), doi: <a href="https://doi.org/10.1016/j.actbio.2023.12.001">https://doi.org/10.1016/j.actbio.2023.12.001</a>, and are made accessible here.</p><p>The provided Fiji macro was written in order to study the cell migration in a spheroid (SPH) doublet fusion experiment. It can be downloaded and adapted or modified to the specific needs of the user, and therefore serves as template for a possible application of Fiji for cell migration analysis. The provided macros can be directly implemented and used in case a similar/comparable experiment is conducted.</p><h3>Methodology</h3><p>The "batch_process_ROI_generator.ijm"- file is applied to the dataset of interest first to define the needed regions of interest (ROI), in our case spheroid doublets on day 0, and follows following methodology:</p><p>User input to define input and output folder</p><p>Generation of a maximum intensity projection of the input z-stacks</p><p>Channel separation and application of a blurring filter and masking of the image based on the fluorescent signal</p><p>Circle fitting based on the outline of the masked region</p><p>The left most pixel of the circle is defined as center of the fusion area (remark: this applies, since in all images of the used dataset the GFP-labeled SPH/S-SPHs was present on the right side of the fusion area)</p><p>Automatic definition of three region of interests (ROIs) where one is centered on the identified center of the fusion area, and two neighboring areas covering both sides of the fusion area</p><p>Saving the ROIs in a designated output folder.</p><p>Using "batch_process_Analysis.ijm"-file to apply the defined ROIs of each sample to the corresponding sample to measure the mean fluorescent intensity of each ROI. The "batch_process_Analysis.ijm" gives the option to define input and output, displays the applied ROI and measures the intended features (here mean intensity fluorescence). The measured data can be saved and used for downstream analysis.</p><h3>Technical details</h3><p>The dataset consists of three files:</p><ol><li>README.txt</li><li>batch_process_ROI_generator.ijm</li><li>batch_process_Analysis.ijm</li></ol><p>While "batch_process_ROI_generator.ijm"-file is used to define the regions of interest (ROI) depending on the GFP-signal of the LSM-image z-stack the second script uses the defined ROIs (that can be edited before application) to read out the intended parameters for analysis (here the mean fluorescent intensity).</p><p>The Fiji macro was written to be applied to z-stack image data taken on an LSM 800 (Zeiss, Germany). File format input: .czi</p><p>The code is commented to allow an easy adaptation to other requirements and to facilitate the overall comprehensibility.</p><p>Software used and needed for image analysis is Fiji:</p><p>Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., … Cardona, A. (2012). Fiji: an open-source platform for biological-image analysis. Nature Methods, 9(7), 676–682.<a href="https://doi.org/10.1038/nmeth.2019"> doi:10.1038/nmeth.2019</a></p><p>Language: English</p><h3>Further details</h3><p>In case the dataset is used for scientific work/publication please cite the following article: </p><p>"Scaffolded spheroids as building blocks for bottom-up cartilage tissue engineering show enhanced bioassembly dynamics" by O.Kopinski-Grünwald and O.Guillaume et al. (2023), doi: <a href="https://doi.org/10.1016/j.actbio.2023.12.001">https://doi.org/10.1016/j.actbio.2023.12.001</a></p>
3D pointcloud for plan creation [octree 0.01m] Karlskirche, Vienna Austria
No full text<p>pointcloud model [las + e57] of the interior and exterior spaces of Karlskirche, Vienna Austria; <br>primary source laserscan Riegl & TU Wien supplemented with 3D mesh model Meixner ZT GmbH; <br>base material pointcloud octree filtered 0.01m (spatial point distance 0.01m); <br>pointclouds within project coordinate system - transformation matrix to global coordinate system WGS84_EPSG 4978 attached</p>
<p>please contact <strong>[email protected]</strong> for access</p>
<p> </p>
<p> </p><p>interior of cupola captured with terrestrial laserscanner Zoller Fröhlich Imager 5010C;<br>all other areas captured with Riegl VZ 400i; scans colored with RGB camera;<br>geopositioning of Riegl Scans with GNSS-RTK precision (about 0.03m accuracy);<br>data from different scanning campaings joined with Multi-Station-Adjustment in Riegl RiScan Software (ICP-matching);</p><p>pointcloud in local coordinate system (=PRCS) for import into cad-software;<br>transformation matrix to global coordinate system WGS84_EPSG 4978 included in dataset;<br>pointcloud reduction using octree filter with 0.01m cell size resulting in spatial point distance of about 0.01m</p>
3D Reconstruction Model of the Former Synagogue in the Schmalzhofgasse 3, Vienna (1883/84 | Architect: Max Fleischer)
No full text<p>This record contains model data originally created in the framework of the masters' thesis of Georg Niessner & Peter Schilling at TU Wien (2004).</p><p>Facts: Association Synagogue of the Temple Association for the Districts of Mariahilf and Neubau | Erected 1883/84; dedicated on September 9, 1884 | Architect: Max Fleischer | Capacity: seating for 226 women and 322 men | Appearance: similar to the churches built by Friedrich Schmidt in brick–neo-Gothic style; triple-aisled building with implicit double tower façade at the west front</p><p>See also:</p><p>* City Guide --> https://www.lit-verlag.de/isbn/978-3-643-90170-5</p><p>* Locations for comparison:</p><p>- Müllnergasse 21 - 1090 Vienna</p><p>- Neudeggergasse 12 - 1080 Vienna</p><p> </p><p>The data set includes</p><p>- Modelling software: ArchiCAD *.PLA - Archive</p><p>- Rendering Software: ArtLantis *.ATLA - Archive</p><p>- Panoramic representation: *.HTML & *.PNO</p><p> </p>
3D mesh model Karlskirche, Vienna Austria
No full text<p>mesh model interior and exterior created by laserscan and photogrammetry</p><p>please contact <a href="mailto:[email protected]">[email protected]</a> for access</p><p>captured with Zoller Fröhlich Imager 5010C with HDR 80mpx camera; processed within local coordinate system; supplemented with photogrammetry using calibrated camera (undefined model) and 12mpx UAV camera; matched with Riegl (Riegl LMS & TU Wien) dataset using point sampling and ICP matching; </p><p>coordinate system WGS84_EPSG 4978; transformation matrix to local coordinate system of capturing campaign included in dataset</p>
3D Reconstruction Model of the Former Synagogue in the Dirmhirngasse 112, Vienna (1900 | Architect: Richard Esriel)
No full text<p>This record contains model data originally created in the framework of the masters' thesis of Franziska Graber at TU Wien (2009).</p><p>Facts: Association synagogue of Minjan Bethausverein (orthodox prayer house association) | Erected 1900 | Architect: Richard Esriel | Capacity: seating for 120 women and 120 men | Appearance: single-storey building with a compact tower at either side</p><p>See also:</p><p>* City Guide --> https://www.lit-verlag.de/isbn/978-3-643-90170-5</p><p> </p><p>The data set includes</p><p>- Modelling software: ArchiCAD *.PLA - Archive</p><p>- Rendering Software: ArtLantis *.ATLA - Archive</p><p>- Panoramic representation: *.HTML & *.PNO</p><p> </p>
Numerical results for "Non-linear responses and three-particle correlators in correlated electron systems exemplified by the Anderson impurity model"
No full text<p>ℹ️ Access to the files of this version is restricted since figures under APS copyright were uploaded accidentally.</p><p>This dataset contains the numerical data and plot scripts to reproduce the figures from the manuscript "Non-linear responses and three-particle correlators in correlated electron systems exemplified by the Anderson impurity model" submitted for publication to <a href="https://journals.aps.org/prb/">Physical Review B</a> and already available as <a href="https://arxiv.org/abs/2212.11877">preprint on arXiv</a>. See the README file for more details.</p>
Data set for "Investigating the Readability of Test Code: Combining Scientific and Practical Views"
No full text<p>Purpose. The readability of software code is key for understanding and maintaining software systems and tests. Although several studies focus on investigating the readability of software code, we observed limited research work that focuses on the readability of software test code. In industry practice, a limited number of guidelines aim for improving and assessing the readability of software (test) code.</p><p>Objective.Therefore, in this paper, we aim at investigating the readability of test code from an academic perspective complemented by practical views, discussed in grey literature. Furthermore, we conducted a controlled experiment in academic environment to investigate the readability of selected test cases based on combined scientific and practical views. </p><p>Methods. First, we build on the Systematic Mapping Study (SMS) approach with focus on academic literature, complemented by practical aspects reported in grey literature. Second we investigate the perception of readability and understandability in a controlled experiment in academic environment.</p><p>Results. The result set of the SMS includes 19 studies for further analysis. The analysis of grey literature includes 62 results. Based on these sources, we identified a set of commonly agreed influence factors that are relevant for academia and industry but also smaller sets of factors that are mainly discussed in academia or industry with limited overlap. For a selected set of test cases we conducted a controlled experiment to collect knowledge on influence factors and the perception on the readability of test cases. For half of the test cases we showed that selected influence factors have a significant impact on the readability. </p><p>Conclusion. The readability of test code is of interest in academia and industry practice. The results of the reported studies showed a common consensus on a set of influence factors to assess the readability of software test code. However, we also found factors that are more relevant for academia and others that are more relevant for industry. Based on the results, we see the need to bring together academic and industry viewpoints to achieve a common view on the readability of software test code</p><p>The data set includes (a) Mapping Table for the systematic Mapping study, (b) Mapping Table for grey literature analysis, (c) Participant's experience data, (d) Participant's readability assessment data, and (e) Experimental package with selected test cases</p><p><strong>Subject / Keywords: </strong>Test Code · Readability · Understandability · Maintainability · Systematic Mapping Study · Grey Literature · Controlled Experiment</p>
RAAV - Collected data from mobility diaries from people surveyed in the RAAV project.
No full text<h2>General description</h2><p>The project <strong>"Rural Accessibility and Automated Vehicles (RAAV)"</strong> project aims to investigate the impacts on individual accessibility through the implementation of automated vehicles in public transport systems in remote areas. By interviewing more than 200 people in the municipalities of Sooß (Austria) and Mühlwald (Italy) the RAAV project was able to collect individual travel diaries collecting detailed information about and mobility behaviour as well as travel preferences and attitudes.</p><h3>Context and methodology</h3><p>The interviews were done personally together with each individual. The answers were marked and collected by the interviewers in a template. The information later was transferred into a data table.</p><p>Respondents reconstructed their typical one-weekday activity diary. The activities and trips they typically perform have been listed in chronological order indicating their location, timing, and activity category. Moreover, they have indicated the level of obligation of the activities. For each trip, information regarding the typical mode, travel time, route and stopovers have been collected. The second part of the questionnaire collected socio-demographic, geographic, transport-related and attitudinal data. Moreover, the level of importance of and satisfaction with a set of PT characteristics (like frequency, network coverage, or stop distance) has been asked according to the requirements of the accessibility model used in this project.</p><p>The data presented is fundamental to multiple articles and papers published in the RAAV project. In order to be as transparent as possible, we want to ensure the public availability of the data.</p><h3>Technical details</h3><p>The dataset contains one Microsoft Excel file containing multiple data sheets. All data from both regions, Mühlwald and Sooß were cumulated. In order to ensure data protection and anonymisation all names, addresses and coordinates of interviewed people, origins and destinations have been deleted from the dataset.</p><p>Other than Microsoft Excel, there is no additional software needed to investigate the data. The first datasheet gives an overview of abbreviations and data stored in each data sheet. </p>
Eggshapes: A collection of egg-shaped objects and their boundaries
No full text<h2>Egg shapes</h2><p>A collection of egg-shaped objects and their boundaries.</p><h2>Creators</h2><ul><li><a href="mailto:[email protected]">Vincent Pelletier</a></li><li><a href="mailto:[email protected]">Jiří Hladůvka</a></li></ul><h2>Introduction</h2><p>Egg shapes are generalized ellipses with positively weighted foci [1]. They can describe a wide range of natural and artificial objects that deviate from the standard ellipse model, such as eggs, avocados, leaves, and rackets.</p><p>Fitting egg shapes to these objects is a challenging task that may find many applications in computer vision, image analysis, and pattern recognition. However, there is a lack of publicly available collections of real egg-shaped objects that can be used for developing and testing egg shape-fitting algorithms.</p><p>This collection aims to fill this gap by providing a diverse set of images, segmentation masks, and boundaries of real egg-shaped objects.</p><h2>Context and methodology</h2><p>The purpose of this collection is to:</p><ul><li>demonstrate the existence of objects that are better described by egg shapes rather than by ellipses, and</li><li>serve as a test collection for the development of egg shape-fitting algorithms.</li></ul><h3>Diversity and quality</h3><p>This collection consists of seven datasets:</p><ul><li>eggs_whole: 1,100 whole-egg photographs and segmentation masks from the <a href="https://universe.roboflow.com/the-nho/egg-segmentation">Egg-segmentation Dataset</a> [2]. We augmented them with 1,100 boundary-coordinates text files.</li><li>eggs_boiled: Images of longitudinally halved, hard-boiled eggs found on the internet were manually segmented, yielding 12 boundaries each for the egg whites and yolks.</li><li>avocados: Images of longitudinally halved avocados were found on the internet. The shells of these avocados were manually segmented, resulting in 6 boundaries. Some of them are slightly deformed.</li><li>leaves: Leaves from trees and plants were deliberately selected and photographed by authors. The selection criteria included being longitudinally symmetrical, egg-shaped, elongated, and possibly pointed. Manual segmentation excluded the stems and produced 23 boundaries.</li><li>cells: Palisade cells of Arabidopsis thaliana in a micro-CT cross-section slice from <a href="https://waters-gateway.boku.ac.at/">Water's Gateway to Heaven</a> project were manually segmented, resulting in 159, mostly elliptic boundaries.</li><li>household: 11 spoon heads and 2 toilet seats were photographed and segmented by the authors.</li><li>rackets: Images of tennis, badminton, and squash racket heads sourced from the internet were segmented, resulting in 12 boundaries. The outer shell of the squash head is noted to be pointed. One of the tennis heads is elliptic.</li></ul><p>The collection contains a total of 1,129 image+mask pairs and 1,337 boundaries. The images vary in size, resolution, quality, and background. The shapes vary in aspect ratio, eccentricity, curvature, and smoothness.</p><p>While the collection covers a range of natural and artificial domains, it is by no means complete. It can be expected that the set of real-world egg shapes is much broader.</p><p>The collection may have some biases and limitations, such as the subjective selection of objects and the manual segmentation of masks.</p><h3>Organization of files</h3><p>This collection contains files of three types:</p><ol><li>jpg: photographs,</li><li>png: segmentation masks, and</li><li>txt: boundary coordinates.</li></ol><p>Each of the seven datasets has photos and segmentation masks stored in:</p><ul><li>images/{dataset}/{photo}.jpg - photo</li><li>images/{dataset}/{photo}.png - segmentation mask</li></ul><p>Several objects may be segmented from one image. This means one or several boundaries are associated with one image. These boundaries are stored in:</p><ul><li>boundaries/{dataset}/{photo}_{bID}.txt</li></ul><p>where {bID} is a 3-digit boundary identifier.</p><h2>Acknowledgments</h2><ul><li><a href="https://waters-gateway.boku.ac.at/">Water's Gateway to Heaven</a> project for providing the leaf scan,</li><li>Táňa Hladůvková for help with collecting the leaves.</li></ul><h2>Access</h2><ul><li>The collection can be retrieved as a zip file via the following DOI: <a href="https://doi.org/10.48436/de66n-2pj41">10.48436/de66n-2pj41</a>.</li></ul><h2>License</h2><p><a href="https://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International</a>.</p><h2>References</h2><p>[1] Gabdulkhakova, A., Kropatsch, W.G.: Generalized conics with the sharp corners. In: Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications. pp. 419–429, (2021), DOI:<a href="https://doi.org/10.1007/978-3-030-93420-0_39">10.1007/978-3-030-93420-0_39</a>.</p><p>[2] Nho, T.: Egg-segmentation Dataset. In: Roboflow Universe, (2023). <a href="https://universe.roboflow.com/the-nho/egg-segmentation">https://universe.roboflow.com/the-nho/egg-segmentation</a>.</p><p>[3] Hladůvka, J. and Kropatsch, W. G. Fitting egg-shapes to discretized object boundaries. In: <i>Discrete geometry and mathematical morphology</i>, pp. 107–119, (2024), DOI:<a href="https://doi.org/10.1007/978-3-031-57793-2_9">10.1007/978-3-031-57793-2_9</a>. </p><p> </p>
Custom Escape Route Test Model in IFC format
No full text<h2>Description</h2><p>The published data is a digital building model (BIM model) in the IFC format (Industry Foundation Classes).<br>The IFC model represents a custom-developed fictional test model. It was created by researchers from the TU Wien Research Unit Digital Building Process.</p><h3>Context and methodology</h3><ul><li>The IFC model was created as test model to validate the newly developed automated Escape Route Analysis for Vienna's BIM-based building permission process.</li><li>The custom escape route test model is a fictional five-storey building that contains test scenarios for the requirements for escape routes arising from the relevant building regulations. These include start doors and start rooms with several different escape routes, interconnected spaces, an underground parking garage, and different dimensions of the elements along the routes.</li><li>The model was created with the modeling software Archicad 26 and was exported to IFC4 (Reference View).</li></ul><h3>Technical details</h3><ul><li>The dataset includes one BIM model in the IFC format (.ifc).</li><li>It can be used in any software that supports the IFC format.</li></ul>