Browsing by Subject "IMAGE"

Sort by: Order: Results:

Now showing items 1-15 of 15
  • Ritchie, Alexandra; Laitinen, Suvi; Katajisto, Pekka; Englund, Johanna I. (2022)
    Techniques to acquire and analyze biological images are central to life science. However, the workflow downstream of imaging can be complex and involve several tools, leading to creation of very specialized scripts and pipelines that are difficult to reproduce by other users. Although many commercial and open-source software are available, non-expert users are often challenged by a knowledge gap in setting up analysis pipelines and selecting correct tools for extracting data from images. Moreover, a significant share of everyday image analysis requires simple tools, such as precise segmentation, cell counting, and recording of fluorescent intensities. Hence, there is a need for user-friendly platforms for everyday image analysis that do not require extensive prior knowledge on bioimage analysis or coding. We set out to create a bioimage analysis software that has a straightforward interface and covers common analysis tasks such as object segmentation and analysis, in a practical, reproducible, and modular fashion. We envision our software being useful for analysis of cultured cells, histological sections, and high-content data.
  • Su, Peifeng; Tarkoma, Sasu; Pellikka, Petri K. E. (2020)
    Hundreds of narrow bands over a continuous spectral range make hyperspectral imagery rich in information about objects, while at the same time causing the neighboring bands to be highly correlated. Band selection is a technique that provides clear physical-meaning results for hyperspectral dimensional reduction, alleviating the difficulty for transferring and processing hyperspectral images caused by a property of hyperspectral images: large data volumes. In this study, a simple and efficient band ranking via extended coefficient of variation (BRECV) is proposed for unsupervised hyperspectral band selection. The naive idea of the BRECV algorithm is to select bands with relatively smaller means and lager standard deviations compared to their adjacent bands. To make this simple idea into an algorithm, and inspired by coefficient of variation (CV), we constructed an extended CV matrix for every three adjacent bands to study the changes of means and standard deviations, and accordingly propose a criterion to allocate values to each band for ranking. A derived unsupervised band selection based on the same idea while using entropy is also presented. Though the underlying idea is quite simple, and both cluster and optimization methods are not used, the BRECV method acquires qualitatively the same level of classification accuracy, compared with some state-of-the-art band selection methods
  • Makinen, Mauno; Puukko-Viertomies, Leena-Riitta; Lindberg, Nina; Siimes, Martti A.; Aalberg, Veikko (2012)
  • Delayre, C.; Sammaljärvi, J.; Billon, S.; Muuri, E.; Sardini, P.; Siitari-Kauppi, M. (2020)
    This study aims to further develop the C-14-PMMA porosity calculation method with a novel autoradiography technique, the Micro-pattern gas detector autoradiography (MPGDA). In this study, the MPGDA is compared with phosphor screen autoradiography (SPA). A set of rock samples from Martinique Island exhibiting a large range of connected porosities was used to validate the MPGDA method. Calculated porosities were found to be in agreement with ones from the SPA and the triple-weight method (TW). The filmless nature of MPGDA as well as straightforward determination of C-14 radioactivity from the source rock makes the porosity calculation less uncertain. The real-time visualization of radioactivity from C-14 beta emissions by MPGDA is a noticeable improvement in comparison to SPA.
  • Sahle, Ch J.; Mirone, A.; Vincent, T.; Kallonen, A.; Huotari, S. (2017)
    An algorithm to simultaneously increase the spatial and statistical accuracy of X-ray Raman scattering (XRS) based tomographic images is presented. Tomography that utilizes XRS spectroscopy signals as a contrast for the images is a new and promising tool for investigating local atomic structure and chemistry in heterogeneous samples. The algorithm enables the spatial resolution to be increased based on a deconvolution of the optical response function of the spectrometer and, most importantly, it allows for the combination of data collected from multiple analyzers and thus enhances the statistical accuracy of the measured images.
  • Santos-Perez, Isaac; Oksanen, Hanna M.; Bamford, Dennis H.; Goni, Felix M.; Reguera, David; Abrescia, Nicola G. A. (2017)
    Genome packaging and delivery are fundamental steps in the replication cycle of all viruses. Icosahedral viruses with linear double-stranded DNA (dsDNA) usually pacicage their genome into a preformed, rigid procapsid using the power generated by a virus-encoded packaging ATPase. The pressure and stored energy due to this confinement of DNA at a high density is assumed to drive the initial stages of genome ejection. Membrane-containing icosahedral viruses, such as bacteriophage PRD1, present an additional architectural complexity by enclosing their genome within an internal membrane vesicle. Upon adsorption to a host cell, the PRD1 membrane remodels into a proteo-lipidic tube that provides a conduit for passage of the ejected linear dsDNA through the cell envelope. Based on volume analyses of PRD1 membrane vesicles captured by cryo-electron tomography and modeling of the elastic properties of the vesicle, we propose that the internal membrane makes a crucial and active contribution during infection by maintaining the driving force for DNA ejection and countering the internal turgor pressure of the host These novel functions extend the role of the PRD1 viral membrane beyond tube formation or the mere physical confinement of the genome. The presence and assistance of an internal membrane might constitute a biological advantage that extends also to other viruses that package their linear dsDNA to high density within an internal vesicle. (C) 2016 Elsevier B.V. All rights reserved.
  • Rantala, Maaria; Lassas, M.; Sampo, J.; Takalo, J.; Timonen, J.; Siltanen, Mikko Samuli (2014)
  • Van Bavel, Jay J.; Cichocka, Aleksandra; Capraro, Valerio; Sjastad, Hallgeir; Nezlek, John B.; Pavlovic, Tomislav; Alfano, Mark; Gelfand, Michele J.; Azevedo, Flavio; Birtel, Michele D.; Cislak, Aleksandra; Lockwood, Patricia L.; Ross, Robert Malcolm; Abts, Koen; Agadullina, Elena; Aruta, John Jamir Benzon; Besharati, Sahba Nomvula; Bor, Alexander; Choma, Becky L.; Crabtree, Charles David; Cunningham, William A.; De, Koustav; Ejaz, Waqas; Elbaek, Christian T.; Findor, Andrej; Flichtentrei, Daniel; Franc, Renata; Gjoneska, Biljana; Gruber, June; Gualda, Estrella; Horiuchi, Yusaku; Toan Luu Duc Huynh; Ibanez, Augustin; Imran, Mostak Ahamed; Israelashvili, Jacob; Jasko, Katarzyna; Kantorowicz, Jaroslaw; Kantorowicz-Reznichenko, Elena; Krouwel, Andre; Laakasuo, Michael; Lamm, Claus; Leygue, Caroline; Lin, Ming-Jen; Mansoor, Mohammad Sabbir; Marie, Antoine; Mayiwar, Lewend; Mazepus, Honorata; McHugh, Cillian; Minda, John Paul; Mitkidis, Panagiotis; Olsson, Andreas; Otterbring, Tobias; Packer, Dominic J.; Perry, Anat; Petersen, Michael Bang; Puthillam, Arathy; Riano-Moreno, Julian C.; Rothmund, Tobias; Santamaria-Garcia, Hernando; Schmid, Petra C.; Stoyanov, Drozdstoy; Tewari, Shruti; Todosijevic, Bojan; Tsakiris, Manos; Tung, Hans H.; Umbres, Radu G.; Vanags, Edmunds; Vlasceanu, Madalina; Vonasch, Andrew; Yucel, Meltem; Zhang, Yucheng; Abad, Mohcine; Adler, Eli; Akrawi, Narin; Mdarhri, Hamza Alaoui; Amara, Hanane; Amodio, David M.; Antazo, Benedict G.; Apps, Matthew; Ay, F. Ceren; Ba, Mouhamadou Hady; Barbosa, Sergio; Bastian, Brock; Berg, Anton; Bernal-Zarate, Maria P.; Bernstein, Michael; Bialek, Michal; Bilancini, Ennio; Bogatyreva, Natalia; Boncinelli, Leonardo; Booth, Jonathan E.; Borau, Sylvie; Buchel, Ondrej; Cameron, C. Daryl; Carvalho, Chrissie F.; Celadin, Tatiana; Cerami, Chiara; Chalise, Hom Nath; Cheng, Xiaojun; Cian, Luca; Cockcroft, Kate; Conway, Jane; Andres Cordoba-Delgado, Mateo; Crespi, Chiara; Crouzevialle, Marie; Cutler, Jo; Dabrowska, Justyna; Cypryanska, Marzena; Daniels, Michael A.; Davis, Victoria H.; Dayley, Pamala N.; Delouvee, Sylvain; Denkovski, Ognjan; Dezecache, Guillaume; Dhaliwal, Nathan A.; Diato, Alelie B.; Di Paolo, Roberto; Drosinou, Marianna; Dulleck, Uwe; Ekmanis, Janis; Ertan, Arhan S.; Etienne, Tom W.; Farhana, Hapsa Hossain; Farkhari, Fahima; Farmer, Harry; Fenwick, Ali; Fidanovski, Kristijan; Flew, Terry; Fraser, Shona; Frempong, Raymond Boadi; Fugelsang, Jonathan A.; Gale, Jessica; Begona Garcia-Navarro, E.; Garladinne, Prasad; Ghajjou, Oussama; Gkinopoulos, Theofilos; Gray, Kurt; Griffin, Siobhan M.; Gronfeldt, Bjarki; Gumren, Mert; Gurung, Ranju Lama; Halperin, Eran; Harris, Elizabeth; Herzon, Volo; Hruska, Matej; Huang, Guanxiong; Hudecek, Matthias F. C.; Isler, Ozan; Jangard, Simon; Jorgensen, Frederik J.; Kachanoff, Frank; Kahn, John; Dangol, Apsara Katuwal; Keudel, Oleksandra; Koppel, Lina; Koverola, Mika; Kubin, Emily; Kunnari, Anton; Kutiyski, Yordan; Laguna, Oscar; Leota, Josh; Lermer, Eva; Levy, Jonathan; Levy, Neil; Li, Chunyun; Long, Elizabeth U.; Longoni, Chiara; Maglic, Marina; McCashin, Darragh; Metcalf, Alexander L.; Miklousic, Igor; El Mimouni, Soulaimane; Miura, Asako; Molina-Paredes, Juliana; Monroy-Fonseca, Cesar; Morales-Marente, Elena; Moreau, David; Muda, Rafal; Myer, Annalisa; Nash, Kyle; Nesh-Nash, Tarik; Nitschke, Jonas P.; Nurse, Matthew S.; Ohtsubo, Yohsuke; de Mello, Victoria Oldemburgo; O'Madagain, Cathal; Onderco, Michal; Soledad Palacios-Galvez, M.; Palomaki, Jussi; Pan, Yafeng; Papp, Zsofia; Parnamets, Philip; Paruzel-Czachura, Mariola; Pavlovic, Zoran; Payan-Gomez, Cesar; Perander, Silva; Pitman, Michael Mark; Prasad, Rajib; Pyrkosz-Pacyna, Joanna; Rathje, Steve; Raza, Ali; Rego, Gabriel G.; Rhee, Kasey; Robertson, Claire E.; Rodriguez-Pascual, Ivan; Saikkonen, Teemu; Salvador-Ginez, Octavio; Sampaio, Waldir M.; Santi, Gaia C.; Santiago-Tovar, Natalia; Savage, David; Scheffer, Julian A.; Schonegger, Philipp; Schultner, David T.; Schutte, Enid M.; Scott, Andy; Sharma, Madhavi; Sharma, Pujan; Skali, Ahmed; Stadelmann, David; Stafford, Clara Alexandra; Stanojevic, Dragan; Stefaniak, Anna; Sternisko, Anni; Stoica, Augustin; Stoyanova, Kristina K.; Strickland, Brent; Sundvall, Jukka; Thomas, Jeffrey P.; Tinghog, Gustav; Torgler, Benno; Traast, Iris J.; Tucciarelli, Raffaele; Tyrala, Michael; Ungson, Nick D.; Uysal, Mete S.; Van Lange, Paul A. M.; van Prooijen, Jan-Willem; van Rooy, Dirk; Vastfjall, Daniel; Verkoeijen, Peter; Vieira, Joana B.; von Sikorski, Christian; Walker, Alexander Cameron; Watermeyer, Jennifer; Wetter, Erik; Whillans, Ashley; Willardt, Robin; Wohl, Michael J. A.; Wojcik, Adrian Dominik; Wu, Kaidi; Yamada, Yuki; Yilmaz, Onurcan; Yogeeswaran, Kumar; Ziemer, Carolin-Theresa; Zwaan, Rolf A.; Boggio, Paulo S. (2022)
    Changing collective behaviour and supporting non-pharmaceutical interventions is an important component in mitigating virus transmission during a pandemic. In a large international collaboration (Study 1, N = 49,968 across 67 countries), we investigated self-reported factors associated with public health behaviours (e.g., spatial distancing and stricter hygiene) and endorsed public policy interventions (e.g., closing bars and restaurants) during the early stage of the COVID-19 pandemic (April-May 2020). Respondents who reported identifying more strongly with their nation consistently reported greater engagement in public health behaviours and support for public health policies. Results were similar for representative and non-representative national samples. Study 2 (N = 42 countries) conceptually replicated the central finding using aggregate indices of national identity (obtained using the World Values Survey) and a measure of actual behaviour change during the pandemic (obtained from Google mobility reports). Higher levels of national identification prior to the pandemic predicted lower mobility during the early stage of the pandemic (r = -0.40). We discuss the potential implications of links between national identity, leadership, and public health for managing COVID-19 and future pandemics.
  • Rasse, Tobias M.; Hollandi, Reka; Horvath, Peter (2020)
    Various pre-trained deep learning models for the segmentation of bioimages have been made available as developer-to-end-user solutions. They are optimized for ease of use and usually require neither knowledge of machine learning nor coding skills. However, individually testing these tools is tedious and success is uncertain. Here, we present the Open Segmentation Framework (OpSeF), a Python framework for deep learning-based instance segmentation. OpSeF aims at facilitating the collaboration of biomedical users with experienced image analysts. It builds on the analysts' knowledge in Python, machine learning, and workflow design to solve complex analysis tasks at any scale in a reproducible, well-documented way. OpSeF defines standard inputs and outputs, thereby facilitating modular workflow design and interoperability with other software. Users play an important role in problem definition, quality control, and manual refinement of results. OpSeF semi-automates preprocessing, convolutional neural network (CNN)-based segmentation in 2D or 3D, and postprocessing. It facilitates benchmarking of multiple models in parallel. OpSeF streamlines the optimization of parameters for pre- and postprocessing such, that an available model may frequently be used without retraining. Even if sufficiently good results are not achievable with this approach, intermediate results can inform the analysts in the selection of the most promising CNN-architecture in which the biomedical user might invest the effort of manually labeling training data. We provide Jupyter notebooks that document sample workflows based on various image collections. Analysts may find these notebooks useful to illustrate common segmentation challenges, as they prepare the advanced user for gradually taking over some of their tasks and completing their projects independently. The notebooks may also be used to explore the analysis options available within OpSeF in an interactive way and to document and share final workflows. Currently, three mechanistically distinct CNN-based segmentation methods, the U-Net implementation used in Cellprofiler 3.0, StarDist, and Cellpose have been integrated within OpSeF. The addition of new networks requires little; the addition of new models requires no coding skills. Thus, OpSeF might soon become both an interactive model repository, in which pre-trained models might be shared, evaluated, and reused with ease.
  • Kiviruusu, Olli; Konttinen, Hanna; Huurre, Taina; Aro, Hillevi; Marttunen, Mauri; Haukkala, Ari (2016)
    Purpose This study examined the developmental trajectories of self-esteem and body mass index (BMI) from adolescence to mid-adulthood and the way the association between self-esteem and BMI changed during a 26-year follow-up. Methods Participants of a Finnish cohort study in 1983 at 16 years (N = 2194) were followed up at ages 22 (N = 1656), 32 (N = 1471), and 42 (N = 1334) using postal questionnaires. Measures at each time point covered self-esteem and self-reported weight and height. Analyses were done using latent growth curve models (LGM) and difference scores. Results In LGM analyses among females both the initial levels (r = -0.13) and slopes (r = -0.26) of the self-esteem and BMI trajectories correlated negatively. Among males, there were no significant correlations between self-esteem and BMI growth factors. The association between increasing BMI and decreasing self-esteem among females was strongest between ages 22 and 32 (r = -0.16), while among males, increases in BMI and self-esteem correlated positively (r = 0.11) during that period. Among females, cross-sectional correlations between self-esteem and BMI showed an increasing trend (p <0.001) from age 16 (r = -0.07) to age 42 (r = -0.17), whereas among males negative correlation (r = -0.08) emerged only in mid-adulthood at age 42. Conclusion Among females, higher and increasing BMI is associated with lower and more slowly increasing self-esteem. This association is not restricted to adolescent years but persists and gets stronger in mid-adulthood. Among males, associations are weaker but indicate more age-related differences. The results highlight the need for interventions that tackle weight-related stigma and discrimination, especially among women with higher body weight and size.
  • Happonen, Konsta; Aalto, Juha; Kemppinen, Julia; Niittynen, Pekka; Virkkala, Anna-Maria; Luoto, Miska (2019)
    The functional composition of plant communities is a critical modulator of climate change impacts on ecosystems, but it is not a simple function of regional climate. In the Arctic tundra, where climate change is proceeding the most rapidly, communities have not shifted their trait composition as predicted by spatial temperature-trait relationships. Important causal pathways are thus missing from models of trait composition change. Here, we study causes of plant community functional variation in an oroarctic tundra landscape in Kilpisjarvi, Finland. We consider the community-weighted means of plant vegetative height, as well as two traits related to the leaf economic spectrum. Specifically, we model their responses to locally measured summer air temperature, snow conditions, and soil resource levels. For each of the traits, we also quantify the importance of intraspecific trait variation (ITV) for between-community functional differences and trait-environment matching. Our study shows that in a tundra landscape (1) snow is the most influential abiotic variable affecting functional composition, (2) vegetation height is under weak local environmental control, whereas leaf economics is under strong local environmental control, (3) the relative magnitude of ITV differs between traits, and (4) ITV is not very consequential for community-level trait-environment relationships. Our analyses highlight the importance of winter conditions for community functional composition in seasonal areas. We show that winter climate change can either amplify or counter the effects summer warming, depending on the trait.
  • Shakeel, Shabih; Seitsonen, Jani J. T.; Kajander, Tommi; Laurinmaki, Pasi; Hyypia, Timo; Susi, Petri; Butcher, Sarah J. (2013)
    Coxsackievirus A9 (CVA9) is an important pathogen of the Picornaviridae family. It utilizes cellular receptors from the integrin v family for binding to its host cells prior to entry and genome release. Among the integrins tested, it has the highest affinity for v6, which recognizes the arginine-glycine-aspartic acid (RGD) loop present on the C terminus of viral capsid protein, VP1. As the atomic model of CVA9 lacks the RGD loop, we used surface plasmon resonance, electron cryo-microscopy, and image reconstruction to characterize the capsid-integrin interactions and the conformational changes on genome release. We show that the integrin binds to the capsid with nanomolar affinity and that the binding of integrin to the virion does not induce uncoating, thereby implying that further steps are required for release of the genome. Electron cryo-tomography and single-particle image reconstruction revealed variation in the number and conformation of the integrins bound to the capsid, with the integrin footprint mapping close to the predicted site for the exposed RGD loop on VP1. Comparison of empty and RNA-filled capsid reconstructions showed that the capsid undergoes conformational changes when the genome is released, so that the RNA-capsid interactions in the N termini of VP1 and VP4 are lost, VP4 is removed, and the capsid becomes more porous, as has been reported for poliovirus 1, human rhinovirus 2, enterovirus 71, and coxsackievirus A7. These results are important for understanding the structural basis of integrin binding to CVA9 and the molecular events leading to CVA9 cell entry and uncoating.
  • Newham, Elis; Corfe, Ian J.; Brown, Kate Robson; Gostling, Neil J.; Gill, Pamela G.; Schneider, Philipp (2020)
    Cementum is a mineralized dental tissue common to mammals that grows throughout life, following a seasonally appositional rhythm. Each year, one thick translucent increment and one thin opaque increment is deposited, offering a near-complete record of an animal's life history. Male and female mammals exhibit significant differences in oral health, due to the contrasting effects of female versus male sex hormones. Oestrogen and progesterone have a range of negative effects on oral health that extends to the periodontium and cementum growth interface. Here, we use synchrotron radiation-based X-ray tomography to image the cementum of a sample of rhesus macaque (Macaca mulatta) teeth from individuals of known life history. We found that increased breeding history in females corresponds with increased increment tortuosity and less organized cementum structure, when compared to male and juvenile cementum. We quantified structural differences by measuring the greyscale 'texture' of cementum and comparing results using principal components analysis. Adult females and males occupy discrete regions of texture space with no overlap. Females with known pregnancy records also have significantly different cementum when compared with non-breeding and juvenile females. We conclude that several aspects of cementum structure and texture may reflect differences in sexual life history in primates.
  • Gomez-Raya-Vilanova, Miguel V.; Leskinen, Katarzyna; Bhattacharjee, Arnab; Virta, Pasi; Rosenqvist, Petja; Smith, Jake L. R.; Bayfield, Oliver W.; Homberger, Christina; Kerrinnes, Tobias; Vogel, Jörg; Pajunen, Maria; Skurnik, Mikael (2022)
    Yersinia phage YerA41 is morphologically similar to jumbo bacteriophages. The isolated genomic material of YerA41 could not be digested by restriction enzymes, and used as a template by conventional DNA polymerases. Nucleoside analysis of the YerA41 genomic material, carried out to find out whether this was due to modified nucleotides, revealed the presence of a ca 1 kDa substitution of thymidine with apparent oligosaccharide character. We identified and purified the phage DNA polymerase (DNAP) that could replicate the YerA41 genomic DNA even without added primers. Cryo-electron microscopy (EM) was used to characterize structural details of the phage particle. The storage capacity of the 131 nm diameter head was calculated to accommodate a significantly longer genome than that of the 145 577 bp genomic DNA of YerA41 determined here. Indeed, cryo-EM revealed, in contrast to the 25 angstrom in other phages, spacings of 33-36 angstrom between shells of the genomic material inside YerA41 heads suggesting that the heavily substituted thymidine increases significantly the spacing of the DNA packaged inside the capsid. In conclusion, YerA41 appears to be an unconventional phage that packages thymidine-modified genomic DNA into its capsids along with its own DNAP that has the ability to replicate the genome.
  • Repo, J. P.; Homsy, P.; Uimonen, M. M.; Roine, R. P.; Jahkola, T.; Popov, P. (2019)
    Background: Massive weight loss can notably affect patients' health-related quality of life (HRQoL) and body image. Yet, no body contouring specific instruments to assess HRQoL and body image after massive weight loss have been validated in Finnish. The BODY-Q includes 26 independently functioning scales and a single checklist that measure appearance, HRQoL, and experience of care. The aim of the present study was to translate and validate a Finnish version of the BODY-Q among patients who underwent abdominoplasty. Methods: The BODY-Q was translated into Finnish using recommended guidelines. Eighty-two patients who underwent abdominoplasty due to massive weight loss were identified from hospital records using procedure codes. A postal survey including the BODY-Q, the 15D, and general health and pain instruments was used. Criterion validity, Cronbach's alpha, and floor and ceiling effects were analyzed. Results: The BODY-Q translated well into Finnish. Fifty-three patients returned the questionnaires (response rate 65%) and were included. All but the Scars subscale correlated significantly with the 15D mean score, thus indicating strong criterion validity against a generic HRQoL tool. The Excess Skin and the Physical Function scales reached the ceiling effect (>15% of maximum points) in our postoperative sample. No floor effects were observed. Internal consistency of the BODY-Q scales was high (Cronbach's alpha range, 0.81-0.95). Conclusions: The Finnish version of the BODY-Q instrument is equivalent in terms of content, accuracy, and comprehensiveness to the original English version. The findings of the present study indicate that the BODY-Q has psychometric properties suitable for assessing outcomes and treatment effectiveness of abdominoplasty. (C) 2019 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.