ArticleScientific reports2019
OptiJ: Open-source optical projection tomography of large organ samples.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed, 25 citations in OpenAlex.
- Making sense of blobs, whorls, and shades: methods for label-free, inverse imaging in bright-field optical microscopy.Biophysical reviews · 2025Review
- Optical projection tomography implemented for accessibility and low cost (Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2024Article
- Development of Microscopic Techniques for the Visualization of Plant-Root-Knot Nematode Interaction.Plants (Basel, Switzerland) · 2022Article
- Mouse embryo phenotyping using X-ray microCT.Frontiers in cell and developmental biology · 2022Review
- 3D imaging of human organs with micrometer resolution - applied to the endocrine pancreas.Communications biology · 2021Article
- TISSUE CLEARING.Nature reviews. Methods primers · 2021Article
- Multiscale and Multimodal Optical Imaging of the Ultrastructure of Human Liver Biopsies.Frontiers in physiology · 2021Article
- Mesoscopic 3D imaging of pancreatic cancer and Langerhans islets based on tissue autofluorescence.Scientific reports · 2020Article
- zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.Biomedical optics express · 2020Article
- 3D imaging of undissected optically cleared Anopheles stephensi mosquitoes and midguts infected with Plasmodium parasites.PloS one · 2020Article
- Gaussian Light Model in Brightfield Optical Projection Tomography.Scientific reports · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors at 3 institutions in 4 countries.
Funding
Abstract
The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.
Identifiers
What OpenQuestion holds
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.