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Octopi: Open configurable high-throughput imaging platform for infectious disease diagnosis in the field

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Portable Multiplex Optical Assays
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Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation
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Rapid diagnosis of malaria by fluorescence microscopy with light microscope and interference filter
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Drug Resistance in Malaria
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Step-by-step guide to building an inexpensive 3D printed motorized positioning stage for automated high-content screening microscopy
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Cell-Cell Communication between Malaria-Infected Red Blood Cells via Exosome-like Vesicles
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What the WHO's List of Essential Diagnostics means for clinical microbiology laboratories and antimicrobial stewardship practice worldwide
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High-throughput multi-parameter flow-cytometric analysis from micro-quantities of Plasmodium-infected blood
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Lensless digital holographic microscopy and its applications in biomedicine and environmental monitoring
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Chapter 11 DAPI Staining of Fixed Cells for High-Resolution Flow Cytometry of Nuclear DNA
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Broadband Achromatic Metasurface-Refractive Optics
inferredcites →https://doi.org/10.1021/jp501778zopenalex-snapshot
Extending Single-Molecule Microscopy Using Optical Fourier Processing
inferredcites →https://doi.org/10.1021/nn4037706openalex-snapshot
Fluorescent Imaging of Single Nanoparticles and Viruses on a Smart Phone
inferredcites →https://doi.org/10.1023/a:1008045108935openalex-snapshot
Feature Detection with Automatic Scale Selection
inferredcites →https://doi.org/10.1038/d41586-018-05772-zopenalex-snapshot
How to defuse malaria’s ticking time bomb
inferredcites →https://doi.org/10.1038/nmeth929openalex-snapshot
Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
inferredcites →https://doi.org/10.1038/nphoton.2013.187openalex-snapshot
Wide-field, high-resolution Fourier ptychographic microscopy
inferredcites →https://doi.org/10.1038/nrmicro.2017.161openalex-snapshot
Drug resistance in Plasmodium
inferredcites →https://doi.org/10.1038/s41377-019-0129-yopenalex-snapshot
PhaseStain: the digital staining of label-free quantitative phase microscopy images using deep learning
inferredcites →https://doi.org/10.1038/s41467-017-02083-1openalex-snapshot
Malaria parasite DNA-harbouring vesicles activate cytosolic immune sensors
inferredcites →https://doi.org/10.1038/s41551-019-0362-yopenalex-snapshot
Virtual histological staining of unlabelled tissue-autofluorescence images via deep learning
inferredcites →https://doi.org/10.1038/s41564-018-0295-3openalex-snapshot
REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes
inferredcites →https://doi.org/10.1038/s41592-018-0216-7openalex-snapshot
Content-aware image restoration: pushing the limits of fluorescence microscopy
inferredcites →https://doi.org/10.1038/s41592-018-0239-0openalex-snapshot
Deep learning enables cross-modality super-resolution in fluorescence microscopy
inferredcites →https://doi.org/10.1038/s41598-017-01606-6openalex-snapshot
A simple and cost-effective setup for super-resolution localization microscopy
inferredcites →https://doi.org/10.1038/s41598-017-14762-6openalex-snapshot
Characterization of an industry-grade CMOS camera well suited for single molecule localization microscopy – high performance super-resolution at low cost
inferredcites →https://doi.org/10.1038/s41598-018-19149-9openalex-snapshot
Malaria infected red blood cells release small regulatory RNAs through extracellular vesicles
inferredcites →https://doi.org/10.1038/s41598-018-19981-zopenalex-snapshot
Multiplane and Spectrally-Resolved Single Molecule Localization Microscopy with Industrial Grade CMOS cameras
inferredcites →https://doi.org/10.1038/s41598-018-25797-8openalex-snapshot
High-speed Fourier ptychographic microscopy based on programmable annular illuminations
inferredcites →https://doi.org/10.1038/s41598-018-34175-3openalex-snapshot
Unravelling the Role of O-glycans in Influenza A Virus Infection
inferredcites →https://doi.org/10.1038/s41598-019-43845-9openalex-snapshot
Low-cost, sub-micron resolution, wide-field computational microscopy using opensource hardware
inferredcites →https://doi.org/10.1039/c4lc00010bopenalex-snapshot
Mobile phones democratize and cultivate next-generation imaging, diagnostics and measurement tools
inferredcites →https://doi.org/10.1039/c4lc00293hopenalex-snapshot
A paper microfluidic cartridge for automated staining of malaria parasites with an optically transparent microscopy window
inferredcites →https://doi.org/10.1063/1.4941068openalex-snapshot
A one-piece 3D printed flexure translation stage for open-source microscopy
inferredcites →https://doi.org/10.1073/pnas.0900245106openalex-snapshot
Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function
inferredcites →https://doi.org/10.1080/16549716.2017.1337325openalex-snapshot
Point-of-care mobile digital microscopy and deep learning for the detection of soil-transmitted helminths and Schistosoma haematobium
inferredcites →https://doi.org/10.1080/757582976openalex-snapshot
Scale-space theory: a basic tool for analyzing structures at different scales
inferredcites →https://doi.org/10.1103/physrevlett.113.133902openalex-snapshot
Optimal Point Spread Function Design for 3D Imaging
inferredcites →https://doi.org/10.1109/cvpr.2018.00474openalex-snapshot
MobileNetV2: Inverted Residuals and Linear Bottlenecks
inferredcites →https://doi.org/10.1109/cvprw.2017.156openalex-snapshot
The One Hundred Layers Tiramisu: Fully Convolutional DenseNets for Semantic Segmentation
inferredcites →https://doi.org/10.1109/cvprw.2018.00219openalex-snapshot
Ultra Power-Efficient CNN Domain Specific Accelerator with 9.3TOPS/Watt for Mobile and Embedded Applications
inferredcites →https://doi.org/10.1109/ghtc.2015.7344002openalex-snapshot
Automated microscopy and machine learning for expert-level malaria field diagnosis
inferredcites →https://doi.org/10.1109/iccv.2015.123openalex-snapshot
Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification
inferredcites →https://doi.org/10.1109/mpul.2011.942766openalex-snapshot
Perspective on Diagnostics for Global Health
inferredcites →https://doi.org/10.1109/tip.2018.2839891openalex-snapshot
FFDNet: Toward a Fast and Flexible Solution for CNN-Based Image Denoising
inferredcites →https://doi.org/10.1111/joim.12820openalex-snapshot
Smartphone‐based clinical diagnostics: towards democratization of evidence‐based health care
inferredcites →https://doi.org/10.1126/science.1127344openalex-snapshot
Imaging Intracellular Fluorescent Proteins at Nanometer Resolution
inferredcites →https://doi.org/10.1126/science.1260088openalex-snapshot
Expansion microscopy
inferredcites →https://doi.org/10.1126/science.2466341openalex-snapshot
Phylogenetic Stains: Ribosomal RNA-Based Probes for the Identification of Single Cells
inferredcites →https://doi.org/10.1126/science.aaa6090openalex-snapshot
Spatially resolved, highly multiplexed RNA profiling in single cells
inferredcites →https://doi.org/10.1126/science.aaf6644openalex-snapshot
Metalenses at visible wavelengths: Diffraction-limited focusing and subwavelength resolution imaging
inferredcites →https://doi.org/10.1126/science.aat5691openalex-snapshot
Three-dimensional intact-tissue sequencing of single-cell transcriptional states
inferredcites →https://doi.org/10.1126/scitranslmed.3009850openalex-snapshot
Wide-field computational imaging of pathology slides using lens-free on-chip microscopy
inferredcites →https://doi.org/10.1126/scitranslmed.aaa3480openalex-snapshot
Point-of-care quantification of blood-borne filarial parasites with a mobile phone microscope
inferredcites →https://doi.org/10.1126/scitranslmed.aam6310openalex-snapshot
Rapid detection of Mycobacterium tuberculosis in sputum with a solvatochromic trehalose probe
inferredcites →https://doi.org/10.1126/scitranslmed.aar4470openalex-snapshot
Rapid and specific labeling of single live Mycobacterium tuberculosis with a dual-targeting fluorogenic probe
inferredcites →https://doi.org/10.1128/jcm.02155-16openalex-snapshot
Evaluation of the Parasight Platform for Malaria Diagnosis
inferredcites →https://doi.org/10.1128/jcm.02562-16openalex-snapshot
Update on Malaria Diagnostics and Test Utilization
inferredcites →https://doi.org/10.1146/annurev-bioeng-092515-010849openalex-snapshot
Lensless Imaging and Sensing
inferredcites →https://doi.org/10.1177/38.9.1696951openalex-snapshot
Interactions of nucleic acids with fluorescent dyes: spectral properties of condensed complexes.
inferredcites →https://doi.org/10.1186/1471-2121-10-45openalex-snapshot
High-content live cell imaging with RNA probes: advancements in high-throughput antimalarial drug discovery
inferredcites →https://doi.org/10.1186/1475-2875-6-89openalex-snapshot
The use of fluorescence enhancement to improve the microscopic diagnosis of falciparum malaria
inferredcites →https://doi.org/10.1186/s12936-018-2371-9openalex-snapshot
How long do rapid diagnostic tests remain positive after anti-malarial treatment?
inferredcites →https://doi.org/10.1364/boe.6.003210openalex-snapshot
InstantScope: a low-cost whole slide imaging system with instant focal plane detection
inferredcites →https://doi.org/10.1364/oe.23.011394openalex-snapshot
Quantitative differential phase contrast imaging in an LED array microscope
inferredcites →https://doi.org/10.1364/ol.39.001326openalex-snapshot
3D differential phase-contrast microscopy with computational illumination using an LED array
inferredcites →https://doi.org/10.1364/opn.29.7.000034openalex-snapshot
Toward a Thinking Microscope
inferredcites →https://doi.org/10.1364/optica.4.001437openalex-snapshot
Deep learning microscopy
inferredcites →https://doi.org/10.1364/optica.5.000001openalex-snapshot
DiffuserCam: lensless single-exposure 3D imaging
inferredcites →https://doi.org/10.1364/optica.6.000794openalex-snapshot
Deep learning for single-shot autofocus microscopy
inferredcites →https://doi.org/10.1371/journal.pone.0008091openalex-snapshot
A Large Proportion of P. falciparum Isolates in the Amazon Region of Peru Lack pfhrp2 and pfhrp3: Implications for Malaria Rapid Diagnostic Tests
inferredcites →https://doi.org/10.1371/journal.pone.0088977openalex-snapshot
Openstage: A Low-Cost Motorized Microscope Stage with Sub-Micron Positioning Accuracy
inferredcites →https://doi.org/10.1371/journal.pone.0095330openalex-snapshot
Low-Cost Mobile Phone Microscopy with a Reversed Mobile Phone Camera Lens
inferredcites →https://doi.org/10.1371/journal.pone.0096906openalex-snapshot
Quantitative Imaging with a Mobile Phone Microscope
inferredcites →https://doi.org/10.1371/journal.pone.0098781openalex-snapshot
Foldscope: Origami-Based Paper Microscope
inferredcites →https://doi.org/10.1371/journal.pone.0136726openalex-snapshot
Fluorescence In Situ Hybridization (FISH) Assays for Diagnosing Malaria in Endemic Areas
inferredcites →https://doi.org/10.1371/journal.pone.0209827openalex-snapshot
cellSTORM—Cost-effective super-resolution on a cellphone using dSTORM
inferredcites →https://doi.org/10.21037/qims.2019.05.04openalex-snapshot
Rapid and robust whole slide imaging based on LED-array illumination and color-multiplexed single-shot autofocusing
inferredcites →https://doi.org/10.3389/fimmu.2018.01011openalex-snapshot
Monitoring Extracellular Vesicle Cargo Active Uptake by Imaging Flow Cytometry
inferredcites →https://doi.org/10.4103/2153-3539.189698openalex-snapshot
The coming paradigm shift: A transition from manual to automated microscopy
inferredcites →https://doi.org/10.4230/oasics.dx.2026.15openalex-snapshot
AutoResearch Lite: a reproducible paper-inspired experiment runner (Adam mechanism reproduction and convergence-speed comparison)
inferredcites →https://doi.org/10.48550/arxiv.1412.6980openalex-snapshot
Adam: A Method for Stochastic Optimization
inferredcites →https://doi.org/10.48550/arxiv.1510.00149openalex-snapshot
Deep Compression: Compressing Deep Neural Networks with Pruning, Trained Quantization and Huffman Coding
inferredcites →https://doi.org/10.48550/arxiv.1803.11293openalex-snapshot
Deep learning-based virtual histology staining using auto-fluorescence of label-free tissue
inferredcites →https://doi.org/10.57702/o4rdcuwnopenalex-snapshot
World Health Organization
inferredcites →https://doi.org/10.5897/ajpp2018.4942openalex-snapshot
Plasmodium falciparum drug resistance gene status in the Horn of Africa: A systematic review

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Machine learning in the clinical microbiology laboratory: has the time come for routine practice?
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Evaluation of low-cost techniques to detect sickle cell disease and β-thalassemia: an open-label, international, multicentre study
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OpenWorkstation: A modular open-source technology for automated in vitro workflows
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An open-source microscopy framework for simultaneous control of image acquisition, reconstruction, and analysis
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Introducing ARTiMiS: A Low-Cost Flow Imaging Microscope for Microalgal Monitoring
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Digital Protein Detection in Bulk Solutions
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A materials-science perspective on tackling COVID-19
inferred← citeshttps://doi.org/10.1038/s41592-021-01227-yopenalex-snapshot
Imaging Africa: a strategic approach to optical microscopy training in Africa
inferred← citeshttps://doi.org/10.1038/s41592-022-01602-3openalex-snapshot
Open microscopy in the life sciences: quo vadis?
inferred← citeshttps://doi.org/10.1038/s41592-025-02690-7openalex-snapshot
Challenges of microscopy technology dissemination to resource-constrained communities
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Frugal engineering-inspired wearable augmented reality goggle system enables fluorescence-guided cancer surgery
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inferred← citeshttps://doi.org/10.1039/d1em00154jopenalex-snapshot
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Democratizing self-driving labs: advances in low-cost 3D printing for laboratory automation
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An inflatable “finger-lock” for stabilizing nailfold capillary videos and modulating blood flow velocities
inferred← citeshttps://doi.org/10.1073/pnas.2315670121openalex-snapshot
Rapid, antibiotic incubation-free determination of tuberculosis drug resistance using machine learning and Raman spectroscopy
inferred← citeshttps://doi.org/10.1080/10408363.2020.1828811openalex-snapshot
Recent evolutions of machine learning applications in clinical laboratory medicine
inferred← citeshttps://doi.org/10.1093/trstmh/traf070openalex-snapshot
Remoscope: a label-free imaging cytometer for malaria diagnostics
inferred← citeshttps://doi.org/10.1101/2020.09.08.285346openalex-snapshot
Label-free imaging and classification of live P. falciparum
inferred← citeshttps://doi.org/10.1101/2020.12.28.424613openalex-snapshot
Squid: Simplifying Quantitative Imaging Platform Development and Deployment
inferred← citeshttps://doi.org/10.1101/2023.04.19.537544openalex-snapshot
Validating a low-cost, open-source, locally manufactured workstation and computational pipeline for automated histopathology evaluation using deep learning
inferred← citeshttps://doi.org/10.1101/2023.05.31.542706openalex-snapshot
An open-source, high resolution, automated fluorescence microscope
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inferred← citeshttps://doi.org/10.1101/2024.09.21.24314128openalex-snapshot
Morphology-based classification of sickle cell disease and β-thalassemia using a low-cost automated microscope and machine learning
inferred← citeshttps://doi.org/10.1101/2025.10.26.684570openalex-snapshot
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Scoping Review of Deep Learning Techniques for Diagnosis, Drug Discovery, and Vaccine Development in Leishmaniasis
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Malaria misdiagnosis among febrile patients in Senegal: implications for the underestimation of Plasmodium species diversity and malaria burden
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Optical fiber-based homogeneous illumination system for microscopy applications
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009257openalex-snapshot
Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining
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Affordable artificial intelligence-based digital pathology for neglected tropical diseases: A proof-of-concept for the detection of soil-transmitted helminths and Schistosoma mansoni eggs in Kato-Katz stool thick smears
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ESPressoscope: A small and powerful approach for in situ microscopy
inferred← citeshttps://doi.org/10.1515/aot-2021-0013openalex-snapshot
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3D-Printed Portable Robotic Mobile Microscope for Remote Diagnosis of Global Health Diseases
inferred← citeshttps://doi.org/10.3390/mi13050643openalex-snapshot
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