ArticleThe Journal of cell biology2023
Semi-automated 3D fluorescence speckle analyzer (3D-Speckler) for microscope calibration and nanoscale measurement.
Article in The Journal of cell biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Correcting Image Distortion in Expansion Microscopy Using 3D-Aligner.Bio-protocol · 2026Article
- Semi-automated image acquisition and analyses for broad users utilizing macro keyboards.Microscopy (Oxford, England) · 2025Article
- Accurate Identification of Cell Cycle Stages in RPE1 Cells Using the ImmunoCellCycle-ID Method.Bio-protocol · 2025Article
- Article
- One step 4× and 12× 3D-ExM enables robust super-resolution microscopy of nanoscale cellular structures.The Journal of cell biology · 2025Article
- HIV-1 Vif disrupts phosphatase feedback regulation at the kinetochore, leading to a pronounced pseudo-metaphase arrest.bioRxiv : the preprint server for biology · 2024Article
- ImmunoCellCycle-ID - a high-precision immunofluorescence-based method for cell cycle identification.Journal of cell science · 2024Article
- 3D-Aligner: advanced computational tool for correcting image distortion in expansion microscopy.Communications biology · 2024Article
- 3D-Aligner: An advanced computational tool designed to correct image distortion in expansion microscopy for precise 3D reconstitution and quantitative analysis.bioRxiv : the preprint server for biology · 2024Article
- Calibrating Fluorescence Microscopy With 3D-Speckler (3D Fluorescence Speckle Analyzer).Bio-protocol · 2024Article
- ImmunoCellCycle-ID: A high-precision immunofluorescence-based method for cell cycle identification.bioRxiv : the preprint server for biology · 2024Article
- One step 4x and 12x 3D-ExM: robust super-resolution microscopy in cell biology.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The widespread use of fluorescence microscopy has prompted the ongoing development of tools aiming to improve resolution and quantification accuracy for study of biological questions. Current calibration and quantification tools for fluorescence images face issues with usability/user experience, lack of automation, and comprehensive multidimensional measurement/correction capabilities. Here, we developed 3D-Speckler, a versatile, and high-throughput image analysis software that can provide fluorescent puncta quantification measurements such as 2D/3D particle size, spatial location/orientation, and intensities through semi-automation in a single, user-friendly interface. Integrated analysis options such as 2D/3D local background correction, chromatic aberration correction, and particle matching/filtering are also encompassed for improved precision and accuracy. We demonstrate 3D-Speckler microscope calibration capabilities by determining the chromatic aberrations, field illumination uniformity, and response to nanometer-scale emitters above and below the diffraction limit of our imaging system using multispectral beads. Furthermore, we demonstrated 3D-Speckler quantitative capabilities for offering insight into protein architectures and composition in cells.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.