{"entity": "journal", "iuid": "6ec25a367c9645e98240d93d5f88a29b", "timestamp": "2026-10-13T19:21:50.854Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/J%20Microsc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/J%20Microsc"}}, "title": "J Microsc", "issn": "1365-2818", "issn-l": "0022-2720", "publications_count": 4, "publications": [{"entity": "publication", "iuid": "b06ab945973a4d5d8f33e3a79ddb4f75", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b06ab945973a4d5d8f33e3a79ddb4f75.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b06ab945973a4d5d8f33e3a79ddb4f75"}}, "title": "PRIAMOS: A technique for mixing embedding media for freely adjusting pH value and refractive index (RI) for optical clearing (OC) of whole tissue samples.", "authors": [{"family": "Leischner", "given": "Ulrich", "initials": "U"}, {"family": "Reifarth", "given": "Martin", "initials": "M"}, {"family": "Brill", "given": "Monika S", "initials": "MS"}, {"family": "Schmitt", "given": "Florian", "initials": "F"}, {"family": "Hoeppener", "given": "Stephanie", "initials": "S"}, {"family": "Unnersj\u00f6 Jess", "given": "David", "initials": "D"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04321d9fb805493db538489927a42c8f.json"}}, {"family": "Schubert", "given": "Ulrich S", "initials": "US"}, {"family": "Heintzmann", "given": "Rainer", "initials": "R"}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "J Microsc", "issn": "1365-2818", "volume": "300", "issue": "3", "pages": "302-314", "issn-l": "0022-2720"}, "abstract": "Investigations of biological samples often require sample transparency, which is achieved by embedding the sample in a high-refractive index (RI) medium to obtain a homogenous RI distribution in the sample, referred to as optical clearing (OC). Here, we introduce a method for designing embedding media with an increased RI by increasing molecular orbitals, which is achieved by replacing elements in molecules commonly used for OC with elements possessing a more pronounced polarisability. Briefly, we took the established embedding medium Glycerol and exchanged the OH-groups by Thiol-groups, resulting in an embedding medium with very similar properties, but with a higher refractive index. We describe a procedure-abbreviated PRIAMOS-to render biological samples transparent using an RI-matching liquid, which we refer to as pH-value and Refractive Index Adjustment by Mixing highly polarisable molecular Orbital Substances. We focus on optical clearing in three-dimensional tissue samples whilst preserving fluorescence of fluorescent labels. The clearing procedure requires 2-3 days, yielding highly transparent samples, preserving the fluorescence of fluorescent proteins like the yellow fluorescent protein (YFP). This is demonstrated on mouse brain samples, imaged with standard confocal microscopy down to 1.6 mm depth, as well as on kidney samples. Mixtures of monothioglycerol, dithioglycerol and tributylamine achieve RI values between 1.52 and 1.57, and an acidity equivalent to pH values between 5 and 8. Our PRIAMOS approach can serve as a guideline for optimising optical clearing protocols.", "doi": "10.1111/jmi.70022", "pmid": "40778535", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12637013"}], "notes": [], "created": "2026-08-20T11:18:13.303Z", "modified": "2026-09-23T13:23:51.801Z"}, {"entity": "publication", "iuid": "88b04d0f236944a9bdf1bc396885c4a4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/88b04d0f236944a9bdf1bc396885c4a4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/88b04d0f236944a9bdf1bc396885c4a4"}}, "title": "Multi-foci parallelised RESOLFT nanoscopy in an extended field-of-view.", "authors": [{"family": "Casas Moreno", "given": "Xavier", "initials": "X", "orcid": "0000-0002-9583-9022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26b876b7f5094fe6a03880bea27ee0ed.json"}}, {"family": "Pennacchietti", "given": "Francesca", "initials": "F"}, {"family": "Minet", "given": "Guillaume", "initials": "G"}, {"family": "Damenti", "given": "Martina", "initials": "M"}, {"family": "Ollech", "given": "Dirk", "initials": "D", "orcid": "0000-0002-9490-7070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ed240dc445848c099b995a3d27ac1ff.json"}}, {"family": "Barabas", "given": "Federico", "initials": "F"}, {"family": "Testa", "given": "Ilaria", "initials": "I", "orcid": "0000-0003-4005-4997", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e8c6a5d1e3a479e933eb8f143b404fc.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "J Microsc", "issn": "1365-2818", "volume": "291", "issue": "1", "pages": "16-29", "issn-l": "0022-2720"}, "abstract": "Live-cell imaging of biological structures at high resolution poses challenges in the microscope throughput regarding area and speed. For this reason, different parallelisation strategies have been implemented in coordinate- and stochastic-targeted switching super-resolution microscopy techniques. In this line, the molecular nanoscale live imaging with sectioning ability (MoNaLISA), based on reversible saturable optical fluorescence transitions (RESOLFT), offers resolution of large fields of view in a few seconds. In MoNaLISA, engineered light patterns strategically confine the fluorescence to sub-diffracted volumes in a large area and provide optical sectioning, thus enabling volumetric imaging at high speeds. The optical setup presented in this paper extends the degree of parallelisation of the MoNaLISA microscope by more than four times, reaching a field-of-view of 45 - 65 nm$45 - 65\\;{\\rm{nm}}$ . We set up the periodicity and the optical scheme of the illumination patterns to be power-efficient and homogeneous. In a single recording, this new configuration enables super-resolution imaging of an extended population of the post-synaptic density protein Homer1c in living hippocampal neurons. ( 100 - 130 \u03bc m)2${( {100 - 130\\;{\\rm{\\mu m}}} )^2}$", "doi": "10.1111/jmi.13157", "pmid": "36377300", "labels": {"SciLifeLab Fellow": "", "Ilaria Testa": ""}, "xrefs": [], "notes": [], "created": "2022-12-01T18:45:16.178Z", "modified": "2026-09-23T12:54:22.008Z"}, {"entity": "publication", "iuid": "accf75e6d6ca4144806431365dbd76ba", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/accf75e6d6ca4144806431365dbd76ba.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/accf75e6d6ca4144806431365dbd76ba"}}, "title": "Accessing osteocyte lacunar geometrical properties in human jaw bone on the submicron length scale using synchrotron radiation \u03bcCT.", "authors": [{"family": "Hesse", "given": "Bernhard", "initials": "B"}, {"family": "M\u00e4nnicke", "given": "Nils", "initials": "N"}, {"family": "Pacureanu", "given": "Alexandra", "initials": "A"}, {"family": "Varga", "given": "Peter", "initials": "P"}, {"family": "Langer", "given": "Max", "initials": "M"}, {"family": "Maurer", "given": "Peter", "initials": "P"}, {"family": "Peyrin", "given": "Francoise", "initials": "F"}, {"family": "Raum", "given": "Kay", "initials": "K"}], "type": "journal article", "published": "2014-09-00", "journal": {"title": "J Microsc", "issn": "1365-2818", "volume": "255", "issue": "3", "pages": "158-168", "issn-l": "0022-2720"}, "abstract": "The architectural properties of the osteocyte cell network provide a valuable basis for understanding the mechanisms of bone remodelling, mineral homeostasis, ageing and pathologies. Recent advances in synchrotron microtomography enable unprecedented three-dimensional imaging of both the bone lacunar network and the extracellular matrix. Here, we investigate the three-dimensional morphological properties of osteocyte lacunae in human healthy and bisphosphonate-related osteonecrotic jaw bone based on synchrotron X-ray computed tomography images, with a spatial isotropic voxel size of 300 nm. Bisphosphonate-related osteonecrosis of the jaw is a relatively new disease with increasing incidence, which remains poorly understood. A step forward in elucidating this malady is to assess whether, and how, the morphology of the osteocyte lacunar network is modified in the affected jaw tissue. We evaluate thousands of cell lacunae from five specimens of which three originate from patients diagnosed with bisphosphonate-associated osteonecrosis. In this exploratory study, we report three-dimensional quantitative results on lacunar volumes (296-502 \u03bcm(3)), shape (approximated by an ellipsoidal shape with principal axes a > b > c, such that a = 2.2b and a = 4c) and spatial distribution (i.e., 50% of the mineralized matrix volume is located within 12 \u03bcm to the closest lacunar boundary) at submicron resolution on such specimens. We observe that the average lacunar volumes of the bisphosphonate-related osteonecrotic jaw specimens were within the range of volumes found in the two specimens originating from healthy donors and conclude that lacunar volumes are not the key element in the course of bisphosphonate-related osteonecrotic jaw. In three out of five specimens we observe lacunar volume sizes in segmented osteons to be significantly different compared to lacunar volumes in the adjacent tissue regions. Furthermore, we quantify the number of lacunae containing small dense objects (on average 9%). In contrast to lacunar morphology we report the lacunar density (16,000-50,000 per mm(3)) to be different in jaw bone tissue compared to what has been reported in femoral sites.", "doi": "10.1111/jmi.12147", "pmid": "25040055", "labels": [], "xrefs": [], "notes": [], "created": "2018-12-05T11:32:39.440Z", "modified": "2026-08-21T12:19:54.725Z"}, {"entity": "publication", "iuid": "3575f80834dc4754b943af58eb4e36fb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3575f80834dc4754b943af58eb4e36fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3575f80834dc4754b943af58eb4e36fb"}}, "title": "Spatial control of pa-GFP photoactivation in living cells.", "authors": [{"family": "Testa", "given": "I", "initials": "I"}, {"family": "Parazzoli", "given": "D", "initials": "D"}, {"family": "Barozzi", "given": "S", "initials": "S"}, {"family": "Garr\u00e8", "given": "M", "initials": "M"}, {"family": "Faretta", "given": "M", "initials": "M"}, {"family": "Diaspro", "given": "A", "initials": "A"}], "type": "journal article", "published": "2008-04-00", "journal": {"title": "J Microsc", "issn": "1365-2818", "volume": "230", "issue": "Pt 1", "pages": "48-60", "issn-l": "0022-2720"}, "abstract": "Photoactivatable green fluorescent protein (paGFP) exhibits peculiar photo-physical properties making it an invaluable tool for protein/cell tracking in living cells/organisms. paGFP is normally excited in the violet range (405 nm), with an emission peak centred at 520 nm. Absorption cross-section at 488 nm is low in the not-activated form. However, when irradiated with high-energy fluxes at 405 nm, the protein shows a dramatic change in its absorption spectra becoming efficiently excitable at 488 nm. Confocal microscopes allow to control activation in the focal plane. Unfortunately, irradiation extends to the entire illumination volume, making impracticable to limit the process in the 3D (three-dimensional) space. In order to confine the process, we used two advanced intrinsically 3D confined optical methods, namely: total internal reflection fluorescence (TIRF) and two-photon excitation fluorescence (2PE) microscopy. TIRF allows for spatially selected excitation of fluorescent molecules within a thin region at interfaces, i.e. cellular membranes. Optimization of the TIRF optical set-up allowed us to demonstrate photoactivation of paGFP fused to different membrane localizing proteins. Exploitation of the penetration depth showed that activation is efficiently 3D confined even if limited at the interface. 2PE microscopy overcomes both the extended excitation volume of the confocal case and the TIRF constraint of operating at interfaces, providing optical confinement at any focal plane in the specimen within subfemtoliter volumes. The presented results emphasize how photoactivation by non-linear excitation can provide a tool to increase contrast in widefield and confocal cellular imaging.", "doi": "10.1111/j.1365-2818.2008.01951.x", "pmid": "18387039", "labels": {"Ilaria Testa": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "JMI1951"}], "notes": [], "created": "2020-09-29T13:02:09.742Z", "modified": "2022-11-07T11:32:31.791Z"}], "created": "2018-12-05T11:32:39.455Z", "modified": "2020-11-27T13:12:53.341Z"}