Reference library · Living world · Microscopy

Microscopic life & imaging

A micrograph is inseparable from the method that produced it. Preparation, hydration, stain, objective, numerical aperture, contrast mode, focus series and processing can change apparent size and structure. This section pairs method training and primary image archives with specialist atlases and name services. The independent resources included here are exceptions chosen for unusually careful scale, sampling and morphology documentation, not because an attractive gallery is enough.

LIMITS

What this method can and cannot settle

Light microscopy can support a useful morphological description and, for some well-characterised groups, a genus or species. Many bacteria, small protists, diatoms and fungal structures need culture, electron microscopy, chemical or molecular evidence for a defensible species determination. Repository images are comparative evidence rather than a key, and an image-model label is a candidate. State preparation and optical limits, preserve scale and focus depth, and stop where the visible characters stop.

Before you reach for an atlas

Record the characters first.

Matching a photograph against a memory is how misidentifications happen. Working through these in order gives you a description that someone else can check — and that stays useful even if the determination later changes.

Sample and preparation

Record source material, collection method, medium, fixation, stain, mount and whether the subject was living.

Preparation can shrink, swell, flatten, dissolve or selectively retain structures. A measurement is comparable to a reference only when preparation is comparable.
Optical system

Record microscope, objective, numerical aperture, illumination and contrast method.

Magnification alone does not describe resolution. Include camera, pixel size or calibration method and any immersion medium or optical correction used.
Scale and focus depth

Calibrate the image and retain a focus series or z-stack when depth carries characters.

A scale bar added after resizing can be wrong. Preserve the calibration source and raw frames so a reviewer can distinguish surface, internal and out-of-focus structures.
Morphology and movement

Measure several individuals and record shape, structures, arrangement, movement and variability.

One cell may be damaged or atypical. Give units and sample size, and separate observed morphology from an inferred life stage or taxon.
Processing

Declare cropping, stacking, denoising, deconvolution, colour mapping and every other material edit.

Keep the unprocessed source. Processing that improves visibility can also create edges, erase weak structures or make intensities incomparable.

These are the observations. Standards covers the vocabularies that carry them into a record — including Darwin Core for biological occurrences, REMBI and OME for imaging, and ABCD-EFG for geological material — while each observation profile records its own method-specific context. Prepare a contribution covers what to keep alongside the files themselves.

Resources

Grouped by the question you are asking.

A resource can appear under more than one heading. Each entry states who maintains it, what it is best for, and where it stops being reliable.

Describe what you observed

Character guides and controlled terminology, so your description means the same thing to the next reader.

MicroscopyU

Nikon Instruments

A substantial teaching reference for optical principles, contrast methods, fluorescence, digital imaging and common artefacts.

Best for: Understanding what the microscope and contrast method can resolve before interpreting a feature as biological.
Limits: Vendor-authored teaching material, not a taxonomic key, safety course or substitute for the operating manual and training for a particular instrument.
Coverage: General light and fluorescence microscopy, digital imaging and selected advanced methods.
Reuse: Copyright Nikon Instruments; reading is open but content is not blanket-licensed for reuse.
Imaging: Light microscopy

Course or tutorial Open Research pass · 2026-09-02

Diatoms of North America

Collaborative specialist editorial board with institutional and United States agency support

Illustrated genus and species accounts with morphology, terminology, ecology, original references and a practical visual identification system.

Best for: Learning which valve characters to measure and comparing a North American diatom against calibrated specialist imagery.
Limits: North American emphasis and explicitly a work in progress. Taxonomic concepts continue to change, and ecological interpretations may not transfer to other regions.
Coverage: North American freshwater and selected other diatoms, expanding by specialist contribution.
Reuse: Content is copyrighted with page-specific citation and reuse conditions.
Imaging: Light microscopy · Scanning electron microscopy

Identification key Open Research pass · 2026-09-02

Protisten.de

Wolfgang Bettighofer, independent microscopy author

A rigorously documented independent atlas of living protists with microscopy, scale, morphology and sampling information.

Best for: Comparing the movement and living morphology of a protist against carefully scaled, professionally made micrographs.
Limits: An individually maintained, mainly European resource rather than a peer-reviewed database. Taxonomic coverage is selective and every determination still needs specialist corroboration.
Coverage: Mainly European freshwater and other free-living protists, selected by the author.
Reuse: Many records are CC BY-NC-SA 3.0; verify the licence shown on the individual item.
Imaging: Light microscopy

Included as the library's independent exception because scale, preparation and living morphology are documented unusually well; that does not turn it into a nomenclatural authority.

Image atlas Open Research pass · 2026-09-02

Compare against reference evidence

Atlases, catalogues and reference collections for comparing an unknown with documented material or measurements.

BioImage Archive

EMBL-European Bioinformatics Institute

A public archive for publication-associated biological image data across scales and modalities, with dataset-level metadata and accessions.

Best for: Finding primary image evidence behind a paper and comparing methods, metadata and source files rather than screenshots.
Limits: A repository rather than an identification key. Taxonomic depth, metadata completeness, file format, licence and dataset size vary by accession.
Coverage: Biological imaging from molecules and cells to organisms across many modalities.
Reuse: Each dataset states its own licence and terms; check the accession before reuse.
Imaging: Light microscopy · Scanning electron microscopy · Transmission electron microscopy
Contributing: Public discovery and download are open; deposition requires an account and controlled data have additional access conditions.

Data repository Open Research pass · 2026-09-02

Image Data Resource

Open Microscopy Environment project with University of Dundee and EMBL-EBI participation

A curated, searchable collection of published imaging datasets using OME standards and structured annotations, often open to reanalysis.

Best for: Exploring a well-annotated image dataset in the browser and understanding how image, phenotype and experiment metadata connect.
Limits: Selective rather than taxonomically comprehensive, with substantial cell, tissue and screening content. Some legacy images have reduced browser functionality.
Coverage: Curated biological imaging studies across organisms, cells, tissues and experimental screens.
Reuse: Dataset rights and citations are stated per study; software and OME components have separate open-source licences.
Imaging: Light microscopy · Scanning electron microscopy · Transmission electron microscopy

Data repository Open API Research pass · 2026-09-02

EMPIAR

Electron Microscopy Public Image Archive

EMBL-European Bioinformatics Institute

An archive of raw two-dimensional electron micrographs, tilt series, tomograms and volume-EM data underlying published work.

Best for: Inspecting primary electron-microscopy evidence and the acquisition context behind a reconstruction or published figure.
Limits: Files can be enormous and require specialist software. Much of the archive is structural cryo-EM rather than an organism-identification atlas.
Coverage: Electron microscopy datasets across structural, cellular and organismal biology.
Reuse: Public EMPIAR datasets are released under CC0; citation of the accession and associated publication remains expected.
Imaging: Scanning electron microscopy · Transmission electron microscopy

Data repository Open Research pass · 2026-09-02

Nordic Microalgae

Swedish Meteorological and Hydrological Institute through the Swedish Biodiversity Data Infrastructure, with institutional contributors

An illustrated reference for Nordic phytoplankton, cyanobacteria, diatoms, dinoflagellates, ciliates and related protists.

Best for: Comparing a microalgal or plankton observation with curated regional images and occurrence context tied to current names.
Limits: Nordic emphasis and uneven image coverage. Instrument-specific images may not resemble compound light microscopy, and contributed material varies.
Coverage: Nordic marine and freshwater microalgae, cyanobacteria and protists.
Reuse: Media licences vary by contributor; check each record. API data follow the terms stated by the service.
Imaging: Light microscopy · Scanning electron microscopy · Photography

Image atlas Open API Research pass · 2026-09-02

EcoTaxa

Laboratoire d'Océanographie de Villefranche, Sorbonne University and CNRS

A large environment for plankton and particle images from ZooScan, UVP, FlowCam, PlanktoScope and related systems, with annotation and machine-assisted classification.

Best for: Comparing instrument-specific plankton images at scale and seeing how experts organise categories within a project.
Limits: Annotations vary by project, machine predictions are not determinations, and only public projects are visible. Instrument appearance may differ markedly from a compound microscope.
Coverage: Global project-contributed plankton and particle imagery, weighted toward oceanographic imaging systems.
Reuse: Project and image licences vary; inspect the project terms before reuse.
Contributing: Visitors can inspect public material; a free account and project permission are needed for annotation and additional data.

Database Free registration Research pass · 2026-09-02

Diatoms of North America

Collaborative specialist editorial board with institutional and United States agency support

Illustrated genus and species accounts with morphology, terminology, ecology, original references and a practical visual identification system.

Best for: Learning which valve characters to measure and comparing a North American diatom against calibrated specialist imagery.
Limits: North American emphasis and explicitly a work in progress. Taxonomic concepts continue to change, and ecological interpretations may not transfer to other regions.
Coverage: North American freshwater and selected other diatoms, expanding by specialist contribution.
Reuse: Content is copyrighted with page-specific citation and reuse conditions.
Imaging: Light microscopy · Scanning electron microscopy

Identification key Open Research pass · 2026-09-02

Protisten.de

Wolfgang Bettighofer, independent microscopy author

A rigorously documented independent atlas of living protists with microscopy, scale, morphology and sampling information.

Best for: Comparing the movement and living morphology of a protist against carefully scaled, professionally made micrographs.
Limits: An individually maintained, mainly European resource rather than a peer-reviewed database. Taxonomic coverage is selective and every determination still needs specialist corroboration.
Coverage: Mainly European freshwater and other free-living protists, selected by the author.
Reuse: Many records are CC BY-NC-SA 3.0; verify the licence shown on the individual item.
Imaging: Light microscopy

Included as the library's independent exception because scale, preparation and living morphology are documented unusually well; that does not turn it into a nomenclatural authority.

Image atlas Open Research pass · 2026-09-02

Resolve the name or identifier

Authorities that settle an accepted biological or mineral name, astronomical designation or other stable identifier.

Nordic Microalgae

Swedish Meteorological and Hydrological Institute through the Swedish Biodiversity Data Infrastructure, with institutional contributors

An illustrated reference for Nordic phytoplankton, cyanobacteria, diatoms, dinoflagellates, ciliates and related protists.

Best for: Comparing a microalgal or plankton observation with curated regional images and occurrence context tied to current names.
Limits: Nordic emphasis and uneven image coverage. Instrument-specific images may not resemble compound light microscopy, and contributed material varies.
Coverage: Nordic marine and freshwater microalgae, cyanobacteria and protists.
Reuse: Media licences vary by contributor; check each record. API data follow the terms stated by the service.
Imaging: Light microscopy · Scanning electron microscopy · Photography

Image atlas Open API Research pass · 2026-09-02

EcoTaxa

Laboratoire d'Océanographie de Villefranche, Sorbonne University and CNRS

A large environment for plankton and particle images from ZooScan, UVP, FlowCam, PlanktoScope and related systems, with annotation and machine-assisted classification.

Best for: Comparing instrument-specific plankton images at scale and seeing how experts organise categories within a project.
Limits: Annotations vary by project, machine predictions are not determinations, and only public projects are visible. Instrument appearance may differ markedly from a compound microscope.
Coverage: Global project-contributed plankton and particle imagery, weighted toward oceanographic imaging systems.
Reuse: Project and image licences vary; inspect the project terms before reuse.
Contributing: Visitors can inspect public material; a free account and project permission are needed for annotation and additional data.

Database Free registration Research pass · 2026-09-02

Diatoms of North America

Collaborative specialist editorial board with institutional and United States agency support

Illustrated genus and species accounts with morphology, terminology, ecology, original references and a practical visual identification system.

Best for: Learning which valve characters to measure and comparing a North American diatom against calibrated specialist imagery.
Limits: North American emphasis and explicitly a work in progress. Taxonomic concepts continue to change, and ecological interpretations may not transfer to other regions.
Coverage: North American freshwater and selected other diatoms, expanding by specialist contribution.
Reuse: Content is copyrighted with page-specific citation and reuse conditions.
Imaging: Light microscopy · Scanning electron microscopy

Identification key Open Research pass · 2026-09-02

DiatomBase

DiatomBase specialist editors on the WoRMS infrastructure hosted by the Flanders Marine Institute

A global nomenclatural backbone for living and fossil marine and freshwater diatoms, with synonyms, types, literature and selected images.

Best for: Validating the name reached through valve morphology or sequence evidence and tracing its type and literature.
Limits: Primarily nomenclature, not a complete visual key. The service reports substantial unchecked and incompletely illustrated content.
Coverage: Global living and fossil diatoms across marine and freshwater habitats.
Reuse: WoRMS/DiatomBase and record-level terms apply; media licences vary.

Taxonomic authority Open API Research pass · 2026-09-02

Use the right method

Published field, preparation, imaging, measurement and analysis methods, with their limitations and safety requirements.

MicroscopyU

Nikon Instruments

A substantial teaching reference for optical principles, contrast methods, fluorescence, digital imaging and common artefacts.

Best for: Understanding what the microscope and contrast method can resolve before interpreting a feature as biological.
Limits: Vendor-authored teaching material, not a taxonomic key, safety course or substitute for the operating manual and training for a particular instrument.
Coverage: General light and fluorescence microscopy, digital imaging and selected advanced methods.
Reuse: Copyright Nikon Instruments; reading is open but content is not blanket-licensed for reuse.
Imaging: Light microscopy

Course or tutorial Open Research pass · 2026-09-02

MyScope

Microscopy Australia and Australian university partners

Structured training modules and simulators for light, electron and cryogenic microscopy, preparation, analysis and image ethics.

Best for: Learning the workflow and vocabulary of an imaging method before entering a supervised facility or documenting a record.
Limits: Simulators and online modules do not replace facility-specific training, risk assessment or supervised competence with a real instrument and specimen.
Coverage: Light microscopy, SEM, TEM, cryo-EM, focused ion beam and associated preparation and analysis topics.
Reuse: CC BY-SA 4.0 unless a module states otherwise.
Imaging: Light microscopy · Scanning electron microscopy · Transmission electron microscopy

Course or tutorial Open Research pass · 2026-09-02

BioImage Archive

EMBL-European Bioinformatics Institute

A public archive for publication-associated biological image data across scales and modalities, with dataset-level metadata and accessions.

Best for: Finding primary image evidence behind a paper and comparing methods, metadata and source files rather than screenshots.
Limits: A repository rather than an identification key. Taxonomic depth, metadata completeness, file format, licence and dataset size vary by accession.
Coverage: Biological imaging from molecules and cells to organisms across many modalities.
Reuse: Each dataset states its own licence and terms; check the accession before reuse.
Imaging: Light microscopy · Scanning electron microscopy · Transmission electron microscopy
Contributing: Public discovery and download are open; deposition requires an account and controlled data have additional access conditions.

Data repository Open Research pass · 2026-09-02

Image Data Resource

Open Microscopy Environment project with University of Dundee and EMBL-EBI participation

A curated, searchable collection of published imaging datasets using OME standards and structured annotations, often open to reanalysis.

Best for: Exploring a well-annotated image dataset in the browser and understanding how image, phenotype and experiment metadata connect.
Limits: Selective rather than taxonomically comprehensive, with substantial cell, tissue and screening content. Some legacy images have reduced browser functionality.
Coverage: Curated biological imaging studies across organisms, cells, tissues and experimental screens.
Reuse: Dataset rights and citations are stated per study; software and OME components have separate open-source licences.
Imaging: Light microscopy · Scanning electron microscopy · Transmission electron microscopy

Data repository Open API Research pass · 2026-09-02

EMPIAR

Electron Microscopy Public Image Archive

EMBL-European Bioinformatics Institute

An archive of raw two-dimensional electron micrographs, tilt series, tomograms and volume-EM data underlying published work.

Best for: Inspecting primary electron-microscopy evidence and the acquisition context behind a reconstruction or published figure.
Limits: Files can be enormous and require specialist software. Much of the archive is structural cryo-EM rather than an organism-identification atlas.
Coverage: Electron microscopy datasets across structural, cellular and organismal biology.
Reuse: Public EMPIAR datasets are released under CC0; citation of the accession and associated publication remains expected.
Imaging: Scanning electron microscopy · Transmission electron microscopy

Data repository Open Research pass · 2026-09-02

Place it in context

Occurrence, stratigraphic, catalogue and archive services that situate a record in space, time and literature.

BioImage Archive

EMBL-European Bioinformatics Institute

A public archive for publication-associated biological image data across scales and modalities, with dataset-level metadata and accessions.

Best for: Finding primary image evidence behind a paper and comparing methods, metadata and source files rather than screenshots.
Limits: A repository rather than an identification key. Taxonomic depth, metadata completeness, file format, licence and dataset size vary by accession.
Coverage: Biological imaging from molecules and cells to organisms across many modalities.
Reuse: Each dataset states its own licence and terms; check the accession before reuse.
Imaging: Light microscopy · Scanning electron microscopy · Transmission electron microscopy
Contributing: Public discovery and download are open; deposition requires an account and controlled data have additional access conditions.

Data repository Open Research pass · 2026-09-02

Image Data Resource

Open Microscopy Environment project with University of Dundee and EMBL-EBI participation

A curated, searchable collection of published imaging datasets using OME standards and structured annotations, often open to reanalysis.

Best for: Exploring a well-annotated image dataset in the browser and understanding how image, phenotype and experiment metadata connect.
Limits: Selective rather than taxonomically comprehensive, with substantial cell, tissue and screening content. Some legacy images have reduced browser functionality.
Coverage: Curated biological imaging studies across organisms, cells, tissues and experimental screens.
Reuse: Dataset rights and citations are stated per study; software and OME components have separate open-source licences.
Imaging: Light microscopy · Scanning electron microscopy · Transmission electron microscopy

Data repository Open API Research pass · 2026-09-02

EMPIAR

Electron Microscopy Public Image Archive

EMBL-European Bioinformatics Institute

An archive of raw two-dimensional electron micrographs, tilt series, tomograms and volume-EM data underlying published work.

Best for: Inspecting primary electron-microscopy evidence and the acquisition context behind a reconstruction or published figure.
Limits: Files can be enormous and require specialist software. Much of the archive is structural cryo-EM rather than an organism-identification atlas.
Coverage: Electron microscopy datasets across structural, cellular and organismal biology.
Reuse: Public EMPIAR datasets are released under CC0; citation of the accession and associated publication remains expected.
Imaging: Scanning electron microscopy · Transmission electron microscopy

Data repository Open Research pass · 2026-09-02

Nordic Microalgae

Swedish Meteorological and Hydrological Institute through the Swedish Biodiversity Data Infrastructure, with institutional contributors

An illustrated reference for Nordic phytoplankton, cyanobacteria, diatoms, dinoflagellates, ciliates and related protists.

Best for: Comparing a microalgal or plankton observation with curated regional images and occurrence context tied to current names.
Limits: Nordic emphasis and uneven image coverage. Instrument-specific images may not resemble compound light microscopy, and contributed material varies.
Coverage: Nordic marine and freshwater microalgae, cyanobacteria and protists.
Reuse: Media licences vary by contributor; check each record. API data follow the terms stated by the service.
Imaging: Light microscopy · Scanning electron microscopy · Photography

Image atlas Open API Research pass · 2026-09-02

EcoTaxa

Laboratoire d'Océanographie de Villefranche, Sorbonne University and CNRS

A large environment for plankton and particle images from ZooScan, UVP, FlowCam, PlanktoScope and related systems, with annotation and machine-assisted classification.

Best for: Comparing instrument-specific plankton images at scale and seeing how experts organise categories within a project.
Limits: Annotations vary by project, machine predictions are not determinations, and only public projects are visible. Instrument appearance may differ markedly from a compound microscope.
Coverage: Global project-contributed plankton and particle imagery, weighted toward oceanographic imaging systems.
Reuse: Project and image licences vary; inspect the project terms before reuse.
Contributing: Visitors can inspect public material; a free account and project permission are needed for annotation and additional data.

Database Free registration Research pass · 2026-09-02

DiatomBase

DiatomBase specialist editors on the WoRMS infrastructure hosted by the Flanders Marine Institute

A global nomenclatural backbone for living and fossil marine and freshwater diatoms, with synonyms, types, literature and selected images.

Best for: Validating the name reached through valve morphology or sequence evidence and tracing its type and literature.
Limits: Primarily nomenclature, not a complete visual key. The service reports substantial unchecked and incompletely illustrated content.
Coverage: Global living and fossil diatoms across marine and freshwater habitats.
Reuse: WoRMS/DiatomBase and record-level terms apply; media licences vary.

Taxonomic authority Open API Research pass · 2026-09-02

Learn the field

Textbooks, courses and teaching material for building the underlying competence.

MicroscopyU

Nikon Instruments

A substantial teaching reference for optical principles, contrast methods, fluorescence, digital imaging and common artefacts.

Best for: Understanding what the microscope and contrast method can resolve before interpreting a feature as biological.
Limits: Vendor-authored teaching material, not a taxonomic key, safety course or substitute for the operating manual and training for a particular instrument.
Coverage: General light and fluorescence microscopy, digital imaging and selected advanced methods.
Reuse: Copyright Nikon Instruments; reading is open but content is not blanket-licensed for reuse.
Imaging: Light microscopy

Course or tutorial Open Research pass · 2026-09-02

MyScope

Microscopy Australia and Australian university partners

Structured training modules and simulators for light, electron and cryogenic microscopy, preparation, analysis and image ethics.

Best for: Learning the workflow and vocabulary of an imaging method before entering a supervised facility or documenting a record.
Limits: Simulators and online modules do not replace facility-specific training, risk assessment or supervised competence with a real instrument and specimen.
Coverage: Light microscopy, SEM, TEM, cryo-EM, focused ion beam and associated preparation and analysis topics.
Reuse: CC BY-SA 4.0 unless a module states otherwise.
Imaging: Light microscopy · Scanning electron microscopy · Transmission electron microscopy

Course or tutorial Open Research pass · 2026-09-02

Diatoms of North America

Collaborative specialist editorial board with institutional and United States agency support

Illustrated genus and species accounts with morphology, terminology, ecology, original references and a practical visual identification system.

Best for: Learning which valve characters to measure and comparing a North American diatom against calibrated specialist imagery.
Limits: North American emphasis and explicitly a work in progress. Taxonomic concepts continue to change, and ecological interpretations may not transfer to other regions.
Coverage: North American freshwater and selected other diatoms, expanding by specialist contribution.
Reuse: Content is copyrighted with page-specific citation and reuse conditions.
Imaging: Light microscopy · Scanning electron microscopy

Identification key Open Research pass · 2026-09-02

Protisten.de

Wolfgang Bettighofer, independent microscopy author

A rigorously documented independent atlas of living protists with microscopy, scale, morphology and sampling information.

Best for: Comparing the movement and living morphology of a protist against carefully scaled, professionally made micrographs.
Limits: An individually maintained, mainly European resource rather than a peer-reviewed database. Taxonomic coverage is selective and every determination still needs specialist corroboration.
Coverage: Mainly European freshwater and other free-living protists, selected by the author.
Reuse: Many records are CC BY-NC-SA 3.0; verify the licence shown on the individual item.
Imaging: Light microscopy

Included as the library's independent exception because scale, preparation and living morphology are documented unusually well; that does not turn it into a nomenclatural authority.

Image atlas Open Research pass · 2026-09-02

Microscopic life & imaging

Record the characters first.

Sample and preparation

Optical system

Scale and focus depth

Morphology and movement

Processing

Grouped by the question you are asking.

Nothing here matches that.

Describe what you observed

Compare against reference evidence

Resolve the name or identifier

Use the right method

Place it in context

Learn the field

Know this field better than this page does?