OpenSPIM

OpenSPIM

Microscope • 39 papers

⭐ Foundational

The ImageJ ecosystem: An open platform for biomedical image analysis.

Molecular reproduction and development 2015 📊 2,519

SUMMARYTechnology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more‐advanced image processing and analysis techniques. A...

⭐ Foundational

Fiji: an open-source platform for biological-image analysis.

Nature methods 2012 📊 60,852

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries...

💾 Data

Sin3a Associated Protein 130kDa, sap130, plays an evolutionary conserved role in zebrafish heart development.

bioRxiv : the preprint server for biology 2023

Abstract Hypoplastic left heart syndrome (HLHS) is a congenital heart disease where the left ventricle is reduced in size. A forward genetic screen in mice...

🏷️ 2 RRIDs

A high-resolution, easy-to-build light-sheet microscope for subcellular imaging.

eLife 2026 📊 1

Although several open-source, easy-to-assemble light-sheet microscope platforms already exist—such as mesoSPIM, OpenSPIM, and OpenSpin—they are optimized for imaging large specimens and lack the resolution required...

💾 Data 🏷️ 4 RRIDs

Observing ER Dynamics over Long Timescales Using Light Sheet Fluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.) 2024

The recent significant progress in developmental bio-imaging of live multicellular organisms has been greatly facilitated by the development of light sheet fluorescence microscopy (LSFM). Both...

A dual-modality optical coherence tomography and selective plane illumination microscopy system for mouse embryonic imaging.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference 2017

Both optical coherence tomography (OCT) and selective plane illumination microscopy (SPIM) are frequently used in mouse embryonic research for high-resolution three-dimensional imaging. Each of these...

AI-based hardware and software tools in microscopy to boost research in immunology and virology.

Frontiers in immunology 2025 📊 4

The integration of computational advances in microscopy has enhanced our ability to visualise immunological events at scales. However, data generated with these techniques is often...

3D Imaging4D ImagingAiryscan MicroscopyArray TomographyConfocal Laser Scanning MicroscopyCryo-Electron MicroscopyDeconvolution MicroscopyElectron TomographyExpansion MicroscopyFluorescence Correlation SpectroscopyFluorescence Lifetime Imaging MicroscopyFluorescence MicroscopyFocused Ion Beam Scanning Electron MicroscopyHigh-Content ScreeningImmuno-Electron MicroscopyImmunofluorescence MicroscopyIntravital MicroscopyLattice Light Sheet MicroscopyLight Sheet Fluorescence MicroscopyLive Cell ImagingMinimal Photon Fluxes MicroscopyMultiphoton MicroscopyOptical SectioningScanning Electron MicroscopySerial Block-Face Scanning Electron MicroscopySingle-Molecule Localization MicroscopySpinning Disk Confocal MicroscopyStimulated Emission Depletion MicroscopyStructured Illumination MicroscopySuper-Resolution MicroscopySuper-Resolution Optical Fluctuation ImagingTotal Internal Reflection Fluorescence MicroscopyTransmission Electron MicroscopyTwo-Photon Excitation MicroscopyVolume Electron MicroscopyWidefield Fluorescence MicroscopyZ-Stack ImagingNikon NSPARCOpenSPIMEscherichia coliMicroManagerDAPIGFPCell CultureCo-cultureExpansion MicroscopyFixationImmunofluorescenceImmunohistochemistryImmunostainingLive ImagingOrganoidSpheroidTumor SpheroidPrimary AstrocytesPrimary Dendritic CellsPrimary Epithelial CellsPrimary MacrophagesPrimary Natural Killer CellsPrimary NeutrophilsPrimary T CellsNikon NSPARCOpenSPIMCellposeCellProfilerImageJinFormnapariOMEROQuPathSAMscikit-imageSerialEMStarDistU-NetMicroManagerExcelJavaKNIMEPythonRFrancis Crick InstituteUniversity of BernUniversity of ReadingZeiss Airyscan
📋 1 💾 Data

Multidimensional Fluorescence Imaging of Embryonic and Postnatal Mammary Gland Development.

Methods in molecular biology (Clifton, N.J.) 2022 📊 2

Multidimensional fluorescence imaging represents a powerful approach for studying the dynamic cellular processes underpinning the development, function, and maintenance of the mammary gland. Here, we...

Investigating hepatic fibrosis heterogeneity by three-dimensional imaging in metabolic dysfunction-associated steatotic liver disease.

Scientific reports 2025 📊 2

Although liver biopsy is a well-established technique to assess fibrosis it has several limitations, including invasive nature, semi-quantitative assessment methods, significant sampling and observer variability,...

💾 Data

Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development.

BMC developmental biology 2016 📊 3

Abstract Background Selective plane illumination microscopy (SPIM a type of light-sheet microscopy) involves focusing a thin sheet of laser light through a specimen at right...

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