Shareish (Share & Cherish): an open-source, map-based, web platform to foster mutual aid

peer reviewedIn this paper, we introduce the Shareish web platform to foster mutual aid following principles of gift economy and generalized exchange. Its design is grounded in prior work (in C&T, CSCW, and solidarity HCI) and it aims at leveraging community assets through donation, free loan, requests of goods and services, and free event announcements. Authenticated users can visualize localized items on a map or through lists, search with filters, add new content with rich textual and visual descriptions, discuss about specific content with others users, and get notifications when new content is created in their neighborhood. In addition, we evaluate AI technologies to ease content creation. The platform can be easily replicated and improved by grassroots movements or researchers seeking autonomy as its source code is made freely available and its installation relies on modern deployment strategies. A demonstration server is available (https://shareish.org/, see Section Online Resources).11. Sustainable cities and communitie

Integration of MALDI FTICR MSI data with the open-source software Cytomine

editorial reviewedOur skin is constantly exposed to solar radiation, high oxygen levels, and environmental pollutants. Our study aims to target specific native (LipS) and oxidized phospholipids (oxLipS) that are known to be senescence-associated secretory phenotype (SASP) related (i.e., LysoPC, oxPAPC). The production of these oxidized species is obtained after exposure to UV light. Here, we employ MALDI FTICR mass spectrometry imaging (MSI) to visualize and identify lipid species of interest in an organotypic model system and to integrate this data with the open-source software Cytomine.COMULIS COST ACTIO

Cytomine: towards an open and collaborative software platform for digital pathology bridged to molecular investigations

PURPOSE: Digital histology is being increasingly used in research and clinical applications. In parallel new tissue imaging methods (e.g. imaging mass spectrometry) are currently regarded as very promising approaches for better molecular diagnosis in pathology. However, these new data sources are still often underexploited because of the lack of collaborative software to share and correlate information for multimodal analysis. EXPERIMENTAL DESIGN: We followed the open science paradigm to develop new features in our web-based Cytomine software to support next-generation digital pathology bridged to molecular investigations. RESULTS: Our new open-source developments allow to explore whole-slide classical histology with MALDI imaging and to support preprocessing for biomarker discovery using laser microdissection-based microproteomics. CONCLUSIONS AND CLINICAL RELEVANCE: Our updated version of Cytomine is the first open and web-based tool to enable sharing data from classical histology, molecular imaging and cell counting for proteomics preprocessing. It holds good promise to fulfill imminent needs in molecular histopathology. This article is protected by copyright. All rights reserved

BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows

Peer reviewe

BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows

Automated image analysis has become key to extract quantitative information from microscopy images, however the methods involved are now often so complex that they can no longer be unambiguously described using written protocols. We introduce BIAFLOWS, a web based framework to encapsulate, reproducibly deploy, and benchmark automated bioimage analysis workflows. BIAFLOWS helps diffusing and fairly comparing image analysis methods, hence safeguarding research based on their results by enforcing highest quality standards. All rights reserved. No reuse allowed without permission. (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the praeprint in perpetuity