{"entity": "journal", "iuid": "4a1dbd41b5d64fae81027116c8ba0c92", "timestamp": "2026-09-03T05:14:31.047Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/HardwareX.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/HardwareX"}}, "title": "HardwareX", "issn": "2468-0672", "issn-l": null, "publications_count": 2, "publications": [{"entity": "publication", "iuid": "ebfaa67b2a4844258e59e024f64fefab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ebfaa67b2a4844258e59e024f64fefab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ebfaa67b2a4844258e59e024f64fefab"}}, "title": "An open-source microscopy framework for simultaneous control of image acquisition, reconstruction, and analysis.", "authors": [{"family": "Casas Moreno", "given": "Xavier", "initials": "X"}, {"family": "Silva", "given": "Mariline Mendes", "initials": "MM"}, {"family": "Roos", "given": "Johannes", "initials": "J"}, {"family": "Pennacchietti", "given": "Francesca", "initials": "F"}, {"family": "Norlin", "given": "Nils", "initials": "N"}, {"family": "Testa", "given": "Ilaria", "initials": "I"}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "HardwareX", "issn": "2468-0672", "volume": "13", "pages": "e00400", "issn-l": null}, "abstract": "We present a computational framework to simultaneously perform image acquisition, reconstruction, and analysis in the context of open-source microscopy automation. The setup features multiple computer units intersecting software with hardware devices and achieves automation using python scripts. In practice, script files are executed in the acquisition computer and can perform any experiment by modifying the state of the hardware devices and accessing experimental data. The presented framework achieves concurrency by using multiple instances of ImSwitch and napari working simultaneously. ImSwitch is a flexible and modular open-source software package for microscope control, and napari is a multidimensional image viewer for scientific image analysis. The presented framework implements a system based on file watching, where multiple units monitor a filesystem that acts as the synchronization primitive. The proposed solution is valid for any microscope setup, supporting various biological applications. The only necessary element is a shared filesystem, common in any standard laboratory, even in resource-constrained settings. The file watcher functionality in Python can be easily integrated into other python-based software. We demonstrate the proposed solution by performing tiling experiments using the molecular nanoscale live imaging with sectioning ability (MoNaLISA) microscope, a high-throughput super-resolution microscope based on reversible saturable optical fluorescence transitions (RESOLFT).", "doi": "10.1016/j.ohx.2023.e00400", "pmid": "36824447", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9941414"}, {"db": "pii", "key": "S2468-0672(23)00007-X"}], "notes": [], "created": "2026-08-20T08:02:47.901Z", "modified": "2026-08-20T08:02:47.933Z"}, {"entity": "publication", "iuid": "b4dc6f6a567b48f5ac480feaf469a154", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b4dc6f6a567b48f5ac480feaf469a154.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b4dc6f6a567b48f5ac480feaf469a154"}}, "title": "A microfluidic chip carrier including temperature control and perfusion system for long-term cell imaging.", "authors": [{"family": "Cantoni", "given": "Federico", "initials": "F"}, {"family": "Werr", "given": "Gabriel", "initials": "G"}, {"family": "Barbe", "given": "Laurent", "initials": "L"}, {"family": "Porras", "given": "Ana Maria", "initials": "AM"}, {"family": "Tenje", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "HardwareX", "issn": "2468-0672", "volume": "10", "pages": "e00245", "issn-l": null}, "abstract": "Microfluidic devices are widely used for biomedical applications but there is still a lack of affordable, reliable and user-friendly systems for transferring microfluidic chips from an incubator to a microscope while maintaining physiological conditions when performing microscopy. The presented carrier represents a cost-effective option for sustaining environmental conditions of microfluidic chips in combination with minimizing the device manipulation required for reagent injection, media exchange or sample collection. The carrier, which has the outer dimension of a standard well plate size, contains an integrated perfusion system that can recirculate the media using piezo pumps, operated in either continuous or intermittent modes (50-1000 \u00b5l/min). Furthermore, a film resistive heater made from 37 \u00b5m-thick copper wires, including temperature feedback control, was used to maintain the microfluidic chip temperature at 37 \u00b0C when outside the incubator. The heater characterisation showed a uniform temperature distribution along the chip channel for perfusion flow rates up to 10 \u00b5l/min. To demonstrate the feasibility of our platform for long term cell culture monitoring, mouse brain endothelial cells (bEnd.3) were repeatedly monitored for a period of 10 days, demonstrating a system with both the versatility and the potential for long imaging in microphysiological system cell cultures.", "doi": "10.1016/j.ohx.2021.e00245", "pmid": "35607686", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9123440"}, {"db": "pii", "key": "S2468-0672(21)00075-4"}], "notes": [], "created": "2026-08-20T08:02:46.061Z", "modified": "2026-08-20T08:02:46.131Z"}], "created": "2026-08-20T08:02:46.090Z", "modified": "2026-08-20T08:02:46.090Z"}