1,720,961 research outputs found
menoci Software Source Code Distribution, Release 1.1
No full textmenoci Software Source Code Distribution, Release 1.
MedicoSAM: Towards foundation models for medical image segmentation
No full textMedical image segmentation is an important analysis task in clinical practice and research. Deep learning has massively advanced the field, but current approaches are mostly based on models trained for a specific task. Training such models or adapting them to a new condition is costly due to the need for (manually) labeled data. The emergence of vision foundation models, especially Segment Anything, offers a path to universal segmentation for medical images, overcoming these issues. Here, we study how to improve Segment Anything for medical images by comparing different finetuning strategies on a large and diverse dataset. We evaluate the finetuned models on a wide range of interactive and (automatic) semantic segmentation tasks. We find that the performance can be clearly improved for interactive segmentation. However, semantic segmentation does not benefit from pretraining on medical images. Our best model, MedicoSAM, is publicly available at https://github.com/computational-cell-analytics/medico-sam. We show that it is compatible with existing tools for data annotation and believe that it will be of great practical value
From seamless acquisition and sustainable management to publication of next-generation sequencing data
No full textApproaching automation of multiple instance orchestration of the menoci web portal
No full textIntroduction: The menoci web portal addresses the needs of FAIR representation of biomedical basic research data and has been successfully implemented for several large consortia at Göttingen Campus. The operation of multiple menoci instances requires efficient measures to reduce administrative resource efforts. This manuscript describes our approach to automatize server operation and software updating procedures. Methods: The menoci instances are hosted on virtual machines (VM) using IT infrastructure of the local academic IT-service provider. Source code and process documentation is hosted in the Göttingen Campus GitLab service. Continuous Integration/Continuous Delivery (CI/CD) pipelines were developed to routinely build updated Docker images from latest source code revisions and the upstream Drupal Docker image. GitLab functionality for code reviews is employed, using protected branches and the “approval” feature for merge requests. Results: At the beginning, menoci development was mainly driven by the implementation of additional modules, features and optimization of user experience to fulfill the researchers’ requirements. Since the roll out of menoci to an increasing list of research consortia, we additionally focused on improving performance, software quality and enhanced automation processes. Our developed automation pipelines include updates for web server and database components, as well as the Drupal content management system and other components that together form the menoci platform. Furthermore, all menoci code enhancements are automatically distributed to all instances. Success or failing of update processes is monitored systematically to facilitate error handling. All processes are extensively documented to easily integrate new team members into administrative tasks. Discussion: Our experience indicated that automation processes are key to reduce resource efforts for technical administrative tasks. However, a high degree of automation and dependencies invoke the potential of small errors possibly leading to large effects. Therefore, tight quality control by testing and monitoring processes is necessary
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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