Workflow
PhenoPaper separates relevance, publication kind, semantic indexing, paper-linked evidence, and notebook execution. Automated investigation results remain Unverified until reviewed. These jobs can pause independently, so a saved result count does not by itself mean its worker is running now.
These steps identify relevant records and describe the publication type. Relevance and paper kind answer different questions.
API search strategy
Searching only for “plant phenotyping” misses many papers on plant image analysis and trait measurement. Separate search profiles combine field names, plants and organs, measurement technologies, and analysis methods to improve coverage.
The vocabulary and full queries below come from the actual search configuration. The profiles executed depend on the provider, date range, and job settings. Waiting, paused, and retry states are managed separately.
Terms within a vocabulary group use OR. Different groups use AND. Each search profile runs separately instead of combining every term into one large query. Multiword phrases are quoted in Boolean queries.
(plant OR plants OR crop OR crops OR …) AND (imaging OR images OR "computer vision" OR "machine vision" OR …) AND (protocol OR pipeline OR workflow OR framework OR …)Searches for plant phenotyping, crop phenotyping, plant phenomics, and related phrases with OR. This finds papers that use the field's name directly.
OpenAlex · Europe PMC · arXiv
Combines plant context AND imaging/sensors AND methods, or plant context AND traits/growth AND methods. Measurement and analysis papers can qualify even when they do not call themselves phenotyping research.
Europe PMC
Adds fruit, melon, cucumber, and related context to cover fruit image analysis and harvesting localization. Crossref also uses short phrases such as fruit segmentation.
OpenAlex · Europe PMC · arXiv · Crossref
Adds plurals such as plants, leaves, and roots, plus images, illumination, binocular vision, localization/localisation, picking point, and harvesting.
Europe PMC
Combines plant/organ context AND 3D technologies AND measurement/analysis goals. Photogrammetry, SfM/MVS, NeRF, and Gaussian splatting have separate search profiles.
OpenAlex · Europe PMC · arXiv
| Provider | Search scope and retrieval | How to interpret the results |
|---|---|---|
| OpenAlex | Searches titles and abstracts by publication date, retrieving articles, preprints, and reviews. | Uses explicit field-name, fruit vision, and 3D reconstruction profiles. |
| Europe PMC | Searches titles and abstracts using OR within vocabulary groups and AND between them. | Uses broad plant × measurement × method, trait measurement, and spelling-variant profiles. |
| Crossref | Searches bibliographic metadata with short phrases and retrieves relevance-ranked candidates. | This is not a title-only or strict Boolean search. Results are capped per period and query before relevance screening. |
| arXiv | Passes queries and submission-date ranges to the search API. When limited, a date-based OAI-PMH route can retrieve metadata for local phrase matching. | Retrieves candidates using field-name, fruit vision, and 3D reconstruction profiles. |
| bioRxiv | Retrieves metadata pages for a date range. | This scans records rather than running keyword searches. Plant and method context is checked after retrieval, followed by relevance screening. |
These bibliographic searches use short phrases. They run separately from the longer Boolean queries used by other APIs.
Includes English common names, scientific names, singular/plural forms, and abbreviations. Expand a group to see every phrase in the current configuration.
Routine searches include field names, 3D reconstruction, additional fruit profiles, and spelling variants. These are the phrase clauses sent to the APIs; dates and other conditions are added for each provider.
Configured date range: The date range specified by the search job.
Combination: Explicit phenotyping and phenomics terms
("plant phenotyping" OR "crop phenotyping" OR "plant phenomics" OR "crop phenomics" OR "high-throughput phenotyping" OR "field phenotyping" OR "image-based phenotyping" OR "sensor-based phenotyping" OR "digital phenotyping" OR "quantitative phenotyping" OR "functional phenomics" OR microphenotyping)Configured date range: The date range specified by the search job.
Combination: Plants, crops, cultivars, and species AND Imaging, sensors, and measurement AND Methods, automation, and analysis
(plant OR plants OR crop OR crops OR angiosperm OR cereal OR legume OR oilseed OR vegetable OR horticultural OR "fruit tree" OR "forest tree" OR turfgrass OR cultivar OR variety OR genotype OR accession OR germplasm OR "breeding line" OR arabidopsis OR rice OR oryza OR wheat OR triticum OR maize OR corn OR zea OR barley OR hordeum OR soybean OR glycine OR sorghum OR millet OR bean OR phaseolus OR pea OR chickpea OR lentil OR cowpea OR peanut OR groundnut OR rapeseed OR canola OR tomato OR pepper OR capsicum OR eggplant OR potato OR brassica OR grapevine OR vitis OR strawberry OR apple OR citrus OR tea OR coffee OR cassava OR "sweet potato" OR "sugar beet" OR sugarcane OR quinoa OR sunflower OR cotton) AND (imaging OR images OR "computer vision" OR "machine vision" OR microscopy OR hyperspectral OR multispectral OR "thermal imaging" OR "chlorophyll fluorescence" OR spectroscopy OR lidar OR "laser scanning" OR photogrammetry OR photogrammetric OR "structure from motion" OR "multi-view stereo" OR "multiview stereo" OR "stereo vision" OR "multi-view reconstruction" OR "multiview reconstruction" OR "neural radiance field" OR "radiance field" OR "gaussian splatting" OR "3d gaussian splatting" OR 3dgs OR "point cloud" OR "x-ray ct" OR mri OR rgb-d OR sensor OR uav OR drone OR robot OR illumination OR "binocular vision" OR image OR sensing OR microscopic OR fluorescence OR robotic) AND (protocol OR pipeline OR workflow OR framework OR software OR algorithm OR automated OR automation OR non-destructive OR high-throughput OR validation OR calibration OR benchmark OR segmentation OR detection OR classification OR prediction OR counting OR tracking OR reconstruction OR "trait extraction" OR "feature extraction" OR localization OR localisation OR "picking point" OR harvesting)Configured date range: The date range specified by the search job.
Combination: Plants, crops, cultivars, and species AND Traits, growth, stress, and disease AND Methods, automation, and analysis
(plant OR plants OR crop OR crops OR angiosperm OR cereal OR legume OR oilseed OR vegetable OR horticultural OR "fruit tree" OR "forest tree" OR turfgrass OR cultivar OR variety OR genotype OR accession OR germplasm OR "breeding line" OR arabidopsis OR rice OR oryza OR wheat OR triticum OR maize OR corn OR zea OR barley OR hordeum OR soybean OR glycine OR sorghum OR millet OR bean OR phaseolus OR pea OR chickpea OR lentil OR cowpea OR peanut OR groundnut OR rapeseed OR canola OR tomato OR pepper OR capsicum OR eggplant OR potato OR brassica OR grapevine OR vitis OR strawberry OR apple OR citrus OR tea OR coffee OR cassava OR "sweet potato" OR "sugar beet" OR sugarcane OR quinoa OR sunflower OR cotton) AND (phenotype OR phenotyping OR phenotypic OR trait OR traits OR morphology OR architecture OR growth OR stress OR disease OR photosynthetic OR "photosynthetic efficiency" OR "soil moisture" OR germination OR "stomatal density") AND (protocol OR pipeline OR workflow OR framework OR software OR algorithm OR automated OR automation OR non-destructive OR high-throughput OR validation OR calibration OR benchmark OR segmentation OR detection OR classification OR prediction OR counting OR tracking OR reconstruction OR "trait extraction" OR "feature extraction" OR localization OR localisation OR "picking point" OR harvesting)Configured date range: 2016-10-06 onward.
Combination: Additional fruit, orchard, and cucurbit context AND Imaging, sensors, and measurement AND Methods, automation, and analysis
(fruit OR "fruit crops" OR "fruit tree" OR "orchard fruit" OR melon OR watermelon OR cucumber OR cucurbit OR cucurbits OR "cucumis melo" OR "camellia oleifera") AND (imaging OR images OR "computer vision" OR "machine vision" OR microscopy OR hyperspectral OR multispectral OR "thermal imaging" OR "chlorophyll fluorescence" OR spectroscopy OR lidar OR "laser scanning" OR photogrammetry OR photogrammetric OR "structure from motion" OR "multi-view stereo" OR "multiview stereo" OR "stereo vision" OR "multi-view reconstruction" OR "multiview reconstruction" OR "neural radiance field" OR "radiance field" OR "gaussian splatting" OR "3d gaussian splatting" OR 3dgs OR "point cloud" OR "x-ray ct" OR mri OR rgb-d OR sensor OR uav OR drone OR robot OR illumination OR "binocular vision" OR image OR sensing OR microscopic OR fluorescence OR robotic) AND (protocol OR pipeline OR workflow OR framework OR software OR algorithm OR automated OR automation OR non-destructive OR high-throughput OR validation OR calibration OR benchmark OR segmentation OR detection OR classification OR prediction OR counting OR tracking OR reconstruction OR "trait extraction" OR "feature extraction" OR localization OR localisation OR "picking point" OR harvesting)Configured date range: 2016-10-06 onward.
Combination: Plural plant and organ terms AND Imaging, sensors, and measurement AND Methods, automation, and analysis
(plants OR crops OR canopies OR stems OR leaves OR roots OR flowers OR fruits OR seeds OR cells) AND (imaging OR images OR "computer vision" OR "machine vision" OR microscopy OR hyperspectral OR multispectral OR "thermal imaging" OR "chlorophyll fluorescence" OR spectroscopy OR lidar OR "laser scanning" OR photogrammetry OR photogrammetric OR "structure from motion" OR "multi-view stereo" OR "multiview stereo" OR "stereo vision" OR "multi-view reconstruction" OR "multiview reconstruction" OR "neural radiance field" OR "radiance field" OR "gaussian splatting" OR "3d gaussian splatting" OR 3dgs OR "point cloud" OR "x-ray ct" OR mri OR rgb-d OR sensor OR uav OR drone OR robot OR illumination OR "binocular vision" OR image OR sensing OR microscopic OR fluorescence OR robotic) AND (protocol OR pipeline OR workflow OR framework OR software OR algorithm OR automated OR automation OR non-destructive OR high-throughput OR validation OR calibration OR benchmark OR segmentation OR detection OR classification OR prediction OR counting OR tracking OR reconstruction OR "trait extraction" OR "feature extraction" OR localization OR localisation OR "picking point" OR harvesting)Configured date range: 2016-10-06 onward.
Combination: Plants, crops, cultivars, and species AND Additional imaging, lighting, and binocular vision terms AND Methods, automation, and analysis
(plant OR plants OR crop OR crops OR angiosperm OR cereal OR legume OR oilseed OR vegetable OR horticultural OR "fruit tree" OR "forest tree" OR turfgrass OR cultivar OR variety OR genotype OR accession OR germplasm OR "breeding line" OR arabidopsis OR rice OR oryza OR wheat OR triticum OR maize OR corn OR zea OR barley OR hordeum OR soybean OR glycine OR sorghum OR millet OR bean OR phaseolus OR pea OR chickpea OR lentil OR cowpea OR peanut OR groundnut OR rapeseed OR canola OR tomato OR pepper OR capsicum OR eggplant OR potato OR brassica OR grapevine OR vitis OR strawberry OR apple OR citrus OR tea OR coffee OR cassava OR "sweet potato" OR "sugar beet" OR sugarcane OR quinoa OR sunflower OR cotton) AND (images OR illumination OR "binocular vision") AND (protocol OR pipeline OR workflow OR framework OR software OR algorithm OR automated OR automation OR non-destructive OR high-throughput OR validation OR calibration OR benchmark OR segmentation OR detection OR classification OR prediction OR counting OR tracking OR reconstruction OR "trait extraction" OR "feature extraction" OR localization OR localisation OR "picking point" OR harvesting)Configured date range: 2016-10-06 onward.
Combination: Plants, crops, cultivars, and species AND Imaging, sensors, and measurement AND Additional localization and harvesting terms
(plant OR plants OR crop OR crops OR angiosperm OR cereal OR legume OR oilseed OR vegetable OR horticultural OR "fruit tree" OR "forest tree" OR turfgrass OR cultivar OR variety OR genotype OR accession OR germplasm OR "breeding line" OR arabidopsis OR rice OR oryza OR wheat OR triticum OR maize OR corn OR zea OR barley OR hordeum OR soybean OR glycine OR sorghum OR millet OR bean OR phaseolus OR pea OR chickpea OR lentil OR cowpea OR peanut OR groundnut OR rapeseed OR canola OR tomato OR pepper OR capsicum OR eggplant OR potato OR brassica OR grapevine OR vitis OR strawberry OR apple OR citrus OR tea OR coffee OR cassava OR "sweet potato" OR "sugar beet" OR sugarcane OR quinoa OR sunflower OR cotton) AND (imaging OR images OR "computer vision" OR "machine vision" OR microscopy OR hyperspectral OR multispectral OR "thermal imaging" OR "chlorophyll fluorescence" OR spectroscopy OR lidar OR "laser scanning" OR photogrammetry OR photogrammetric OR "structure from motion" OR "multi-view stereo" OR "multiview stereo" OR "stereo vision" OR "multi-view reconstruction" OR "multiview reconstruction" OR "neural radiance field" OR "radiance field" OR "gaussian splatting" OR "3d gaussian splatting" OR 3dgs OR "point cloud" OR "x-ray ct" OR mri OR rgb-d OR sensor OR uav OR drone OR robot OR illumination OR "binocular vision" OR image OR sensing OR microscopic OR fluorescence OR robotic) AND (localization OR localisation OR "picking point" OR harvesting)Configured date range: 2016-10-06 onward.
Combination: Plural plant and organ terms AND Traits, growth, stress, and disease AND Methods, automation, and analysis
(plants OR crops OR canopies OR stems OR leaves OR roots OR flowers OR fruits OR seeds OR cells) AND (phenotype OR phenotyping OR phenotypic OR trait OR traits OR morphology OR architecture OR growth OR stress OR disease OR photosynthetic OR "photosynthetic efficiency" OR "soil moisture" OR germination OR "stomatal density") AND (protocol OR pipeline OR workflow OR framework OR software OR algorithm OR automated OR automation OR non-destructive OR high-throughput OR validation OR calibration OR benchmark OR segmentation OR detection OR classification OR prediction OR counting OR tracking OR reconstruction OR "trait extraction" OR "feature extraction" OR localization OR localisation OR "picking point" OR harvesting)Configured date range: 2016-10-06 onward.
Combination: Plants, crops, cultivars, and species AND Traits, growth, stress, and disease AND Additional localization and harvesting terms
(plant OR plants OR crop OR crops OR angiosperm OR cereal OR legume OR oilseed OR vegetable OR horticultural OR "fruit tree" OR "forest tree" OR turfgrass OR cultivar OR variety OR genotype OR accession OR germplasm OR "breeding line" OR arabidopsis OR rice OR oryza OR wheat OR triticum OR maize OR corn OR zea OR barley OR hordeum OR soybean OR glycine OR sorghum OR millet OR bean OR phaseolus OR pea OR chickpea OR lentil OR cowpea OR peanut OR groundnut OR rapeseed OR canola OR tomato OR pepper OR capsicum OR eggplant OR potato OR brassica OR grapevine OR vitis OR strawberry OR apple OR citrus OR tea OR coffee OR cassava OR "sweet potato" OR "sugar beet" OR sugarcane OR quinoa OR sunflower OR cotton) AND (phenotype OR phenotyping OR phenotypic OR trait OR traits OR morphology OR architecture OR growth OR stress OR disease OR photosynthetic OR "photosynthetic efficiency" OR "soil moisture" OR germination OR "stomatal density") AND (localization OR localisation OR "picking point" OR harvesting)Configured date range: The date range specified by the search job.
Search mode: bibliographic relevance search
plant phenotypingConfigured date range: The date range specified by the search job.
Search mode: bibliographic relevance search
crop phenotypingConfigured date range: The date range specified by the search job.
Search mode: bibliographic relevance search
plant phenomicsConfigured date range: 2016-10-06 onward.
Search mode: bibliographic relevance search
melon segmentationConfigured date range: 2016-10-06 onward.
Search mode: bibliographic relevance search
fruit segmentationConfigured date range: 2016-10-06 onward.
Search mode: bibliographic relevance search
fruit detectionConfigured date range: 2016-10-06 onward.
Search mode: bibliographic relevance search
fruit harvestingConfigured date range: 2016-01-01 onward.
Combination: Plant and organ context for 3D searches AND Photogrammetry and conventional 3D reconstruction AND 3D measurement and trait extraction goals
(plant OR crop OR seedling OR canopy OR tree OR orchard OR fruit OR leaf OR root OR shoot OR stem OR flower OR inflorescence OR panicle OR spike OR seed OR grain OR vegetable) AND (photogrammetry OR photogrammetric OR "structure from motion" OR sfm OR "multi-view stereo" OR "multiview stereo" OR mvs OR "stereo vision" OR "binocular stereo" OR "multi-view reconstruction" OR "multiview reconstruction" OR "image-based 3d reconstruction" OR "3d reconstruction" OR "three-dimensional reconstruction" OR "point cloud reconstruction" OR rgb-d) AND (reconstruction OR measurement OR quantification OR estimation OR extraction OR phenotyping OR phenotype OR phenotypic OR trait OR morphology OR architecture OR segmentation OR counting OR volume OR area OR biomass OR growth OR "digital twin" OR modeling OR modelling)Configured date range: 2020-01-01 onward.
Combination: Plant and organ context for 3D searches AND NeRF and radiance fields AND 3D measurement and trait extraction goals
(plant OR crop OR seedling OR canopy OR tree OR orchard OR fruit OR leaf OR root OR shoot OR stem OR flower OR inflorescence OR panicle OR spike OR seed OR grain OR vegetable) AND ("neural radiance field" OR "neural radiance fields" OR nerf OR "neural field" OR "neural fields" OR "radiance field" OR "radiance fields") AND (reconstruction OR measurement OR quantification OR estimation OR extraction OR phenotyping OR phenotype OR phenotypic OR trait OR morphology OR architecture OR segmentation OR counting OR volume OR area OR biomass OR growth OR "digital twin" OR modeling OR modelling)Configured date range: 2023-01-01 onward.
Combination: Plant and organ context for 3D searches AND Gaussian splatting AND 3D measurement and trait extraction goals
(plant OR crop OR seedling OR canopy OR tree OR orchard OR fruit OR leaf OR root OR shoot OR stem OR flower OR inflorescence OR panicle OR spike OR seed OR grain OR vegetable) AND ("3d gaussian splatting" OR "gaussian splatting" OR "gaussian splats" OR 3dgs) AND (reconstruction OR measurement OR quantification OR estimation OR extraction OR phenotyping OR phenotype OR phenotypic OR trait OR morphology OR architecture OR segmentation OR counting OR volume OR area OR biomass OR growth OR "digital twin" OR modeling OR modelling)Configured date range: 2016-01-01 onward.
Search mode: bibliographic relevance search
plant 3d reconstructionConfigured date range: 2016-01-01 onward.
Search mode: bibliographic relevance search
crop 3d reconstructionConfigured date range: 2016-01-01 onward.
Search mode: bibliographic relevance search
plant photogrammetryConfigured date range: 2020-01-01 onward.
Search mode: bibliographic relevance search
plant neural radiance fieldConfigured date range: 2023-01-01 onward.
Search mode: bibliographic relevance search
plant gaussian splattingConfigured date range: 2016-01-01 onward.
Combination: stomatal_quantification_phrases
("stomata quantification" OR "stomatal quantification" OR "stomatal aperture quantification" OR "stomatal aperture measurement" OR "stomatal pore measurement" OR "stomatal pore segmentation" OR "stomatal opening measurement" OR "stomata image analysis" OR "stomatal image analysis" OR "guard cell measurement" OR "stomatal morphometry" OR "stomata detection" OR "stomatal detection" OR "stoma detection" OR "stomata recognition" OR "stomatal recognition" OR "stomatal counting" OR "stomatal density estimation")Configured date range: 2016-01-01 onward.
Combination: stomatal_subject AND stomatal_geometry AND stomatal_automation
(stoma OR stomata OR stomatal OR "guard cell" OR "guard cells") AND (aperture OR pore OR opening OR area OR width OR length OR quantification OR measurement OR morphometry) AND (software OR program OR tool OR algorithm OR automated OR automatic OR "image analysis" OR "image processing" OR segmentation OR "deep learning" OR "computer vision" OR pipeline OR "high throughput" OR high-throughput)Configured date range: 2016-01-01 onward.
Search mode: bibliographic relevance search
stomata quantificationConfigured date range: 2016-01-01 onward.
Search mode: bibliographic relevance search
stomatal aperture quantificationConfigured date range: 2016-01-01 onward.
Search mode: bibliographic relevance search
stomatal pore measurementConfigured date range: 2016-01-01 onward.
Search mode: bibliographic relevance search
stomata detectionAdministrators can specify additional phrases, existing profiles, providers, and publication dates to search historical records again. Additional phrases use OR and are combined with plant context using AND. For example, fruit segmentation and fruit counting can broaden fruit-analysis coverage.
Each job saves its query conditions, so later configuration changes do not alter that job. To include additional phrases in ongoing routine searches, add them separately to the routine configuration.
After retrieving bibliographic metadata, duplicates are matched using identifiers such as DOI. Non-botanical contexts such as power plant, and corrections, retractions, and newsletter records are excluded. Titles and available abstracts are then screened for relevance to plant phenotyping methods.
Search terms support discovery. Full-text access, paper-specific data/code checks, and execution in Colab are separate downstream stages.
These jobs enrich relevant records independently. Their results have separate queues, evidence, and completion states.
Notebook creation is a separate workflow from /analyze. An investigation result alone is not an AI-verified notebook.
Paper, Tool, Repository, and Evidence are separate records. A link check or readiness assessment is not an execution result, and no automated result is promoted directly to the reviewed Catalog.