©2020 Biological and Chemical Oceanography Data Management Office.Funded by the U.S. National Science Foundation
©2020 Biological and Chemical Oceanography Data Management Office.An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications.
| Dataset Name | PI-Supplied Description | PI-Supplied Name |
|---|---|---|
| ChemTax based chl-a of algal groups from R/V Atlantic Explorer cruises AE1102, AE1118, AE1206, AE1219 in the Sargasso Sea, Bermuda Atlantic Time-Series Station (BATS) from 2011-2012 (Trophic BATS project) | Samples preserved in Lugol’s were settled overnight in a 100 ml sedimentation chamber and enumerated at 400x using a Nikon TS-100 Eclipse inverted microscope | Inverted Microscope |
| Phytoplankton and nutrients from R/V Sagar Kanya, R/V Sagar Sampada SK256, SS263, SS273, SS286 in the N. Arabian Sea from 2009-2011 (Arabian Sea Noctiluca project) | Olympus Inverted microscope (Model IX 50) | Inverted Microscope |
| BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project). | Used to perform isolations | Olympus CKX41 |
| Carbonate chemistry, shell growth, and respiration data from laboratory experiments on California mussel larvae condcuted at the Hatfield Marine Science Center, Newport, OR in 2013 | Shell size was determined by taking photographs of all sampled larvae scored as normally developed using an inverted transmission microscope (Jena Sedival 250-CL coupled to a FujiFilm Digital SLR S5) at 50x magnification and measuring shell lengths (longest axis parallel to shell hinge) on size calibrated images (ImageJ v 1.42). | Inverted transmission microscope |
| Biovolume data from samples obtained on Gould cruise LMG1411 in the Western Antarctica Peninsula during 2014 (Polar Transcriptome project). | Used to perform isolations | Olympus CKX41 |
| Reactive oxygen species are linked to the toxicity of the dinoflagellate Alexandrium spp. to protists | The IX70 inverted tissue culture microscope is a research-level instrument capable of imaging specimens in a variety of illumination modes including brightfield, darkfield, phase contrast, Hoffman modulation contrast, fluorescence, and differential interference contrast. | Olympus IX70 inverted system microscope |
| Influence of predator-prey evolutionary history, chemical alarm-cues and feeding selection on induction of toxin production in a marine dinoflagellate | The IX70 inverted tissue culture microscope is a research-level instrument capable of imaging specimens in a variety of illumination modes including brightfield, darkfield, phase contrast, Hoffman modulation contrast, fluorescence, and differential interference contrast. | Olympus IX70 inverted system microscope |
| A multi-phylum study of grazer-induced paralytic shellfish toxin production in the dinoflagellate Alexandrium fundyense: A new perspective on control of algal toxicity | The IX70 inverted tissue culture microscope is a research-level instrument capable of imaging specimens in a variety of illumination modes including brightfield, darkfield, phase contrast, Hoffman modulation contrast, fluorescence, and differential interference contrast. | Olympus IX70 inverted system microscope |
| Toxin content of Alexandrium catenella in response of nitrogen sources, algal alarm cues, and grazer exposure | The IX70 inverted tissue culture microscope is a research-level instrument capable of imaging specimens in a variety of illumination modes including brightfield, darkfield, phase contrast, Hoffman modulation contrast, fluorescence, and differential interference contrast. | Olympus IX70 inverted system microscope |
| Cell-growth gene expression reveals a direct fitness cost of grazer-induced toxin production in red tide dinoflagellate prey | The IX70 inverted tissue culture microscope is a research-level instrument capable of imaging specimens in a variety of illumination modes including brightfield, darkfield, phase contrast, Hoffman modulation contrast, fluorescence, and differential interference contrast. | Olympus IX70 inverted system microscope |
| Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC project) | Imaging was performed with phasecontrast microscopy (4×, 0.13 NA objective; Nikon Ti-E) at 1 fps over the course of ~10 min using a CMOS camera (Blackfly S, Teledyne FLIR). An example of the gradient generator used can be found in http://dx.doi.org/10.1038/s41567-021-01247-7. | Nikon Ti-E Inverted Microscope |
| Chemotaxis of Pseudoalteromonas haloplanktis towards exudates of phage-infected and control Synechoccocus (VIC project) | Imaging was performed with phase-contrast microscopy (4×; Zeiss AxioObserver) at 1 fps over the course of ~10 min using a CMOS camera (Grasshopper S, Teledyne FLIR). | Zeiss AxioObserver Inverted microscope |
| Chemotaxis of Vibrio alginolyticus towards live phage-infected/control Synechococcus cells (VIC project) | Imaging was performed with phase-contrast microscopy (4×; Zeiss AxioObserver) at 1 fps over the course of ~10 min using a CMOS camera (Grasshopper S, Teledyne FLIR). | Zeiss AxioObserver Inverted microscope |
| Abundance and biomass of ciliates from inverted microscope counts from samples taken on R/V Atlantic Explorer cruises AE1102, AE1118, AE1206, AE1219 in the Sargasso Sea, Bermuda Atlantic Time-Series Station in 2011-2012 (Trophic BATS project) | Ciliate abundance and biomass was determined using bright-field inverted microscopy (Amacher et al. 2009; Neuer and Cowles 1994). A Nikon Elipse TE300 inverted microscope was used at 40x magnification to count the entire slide. | Inverted Microscope |
| Grazing by copepods Calanus pacificus and Acartia hudsonica at low to high pCO2 levels, 2014-2015 (OA-Copepod_PreyQual project) | To perform cell counts, 2014 experiments | |
| Cell volumes were calculated for 8 species of marine cryptophytes grown under full-spectrum, blue, green, or red light during laboratory-based growth experiments in 2018 | Cell sizes performed on Nikon Eclipse TS100 inverted microscope at 200x magnification using non-preserved cells. | Nikon Eclipse TS100 |
| CTD data with chemical and biological discrete samples from R/V Cape Hatteras cruise CH0711 in the Gulf of Mexico; 2007 (GoMX - N2 Fixation project) | Zeiss ICM-405 inverted microscope | Zeiss ICM-405 inverted microscope |
| Diatom growth rates from samples collected on the Gould cruise LMG1411 in the Western Antarctica Peninsula from 2014 (Polar Transcriptomes project) | Used to perform isolations | Olympus CKX41 |
| Reference sequences, genes, and K0 numbers for sampled diatoms on the Laurence Gould (LMG1411) in the Western Antarctica Peninsula during 2014. (Polar Transcriptomes project) | Used to perform isolations | Olympus CKX41 |
| Diatom abundances from phyto and microzooplankton experiments from the RVIB Nathaniel B. Palmer NBP0601 cruise in the Ross Sea, Southern Ocean from 2005-2006 (CORSACS project, Antarctic microzooplankton project) | Samples were enumerated using light microscopy at 400x magnification with a Zeiss Axiovert S100 inverted microscope (Utermohl, 1958). Utermohl, H. 1958. Zur Vervollkommung der quantitativen phytoplankton-methodik. Mitteilungen der Internationalen Vereinigung fur Limnologie 9: 1-38. | Inverted Microscope |
| Dynamic Mode Structure of Active Turbulence Modeling Results from 2019-2022 (VIC project) | For all experiments, bacterial suspensions were imaged with brightfield illumination on an inverted microscope (Nikon Ti-E) using a sCMOS camera (Zyla 5.5, Andor Technology). | Nikon Ti-E Inverted Microscope |
| Herbivorous protist abundances under simultaneous manipulation of temperature and nutrients from the Long-term Plankton Time Series site in Narragansett Bay, RI in 2017 | Nikon Diaphot 300 | |
| Initial prey abundances for copepod grazing experiments in the Kaneohe Bay, HI, May-June 2013 (MEPS 2017) (EAGER: Copepod nauplii project) | ||
| Isolate information on genes found in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula in 2014 (Polar Transcriptomes project). | Used to perform isolations | Olympus CKX41 |
| Lagrangian Structure and Stretching in Bacterial Turbulence Modeling Results from February 2020 (VIC project) | For all experiments, bacterial suspensions were imaged with brightfield illumination on an inverted microscope (Nikon Ti-E) using a sCMOS camera (Zyla 5.5, Andor Technology) at 40x magnification. | Nikon Ti-E Inverted microscope |
| Concentration of inorganic nutrients, primary productivity measurements and phytoplankton cell concentration in seawater samples from the Malaspina 2010 Circumnavigation Expedition (VitaMaps project) | Approximately 250 cm3 of water were placed in a glass bottle and fixed with hexamine-buffered formaldehyde solution (4% final formalin concentration). A 100 cm3 composite chamber was filled with sample water and its content was allowed to settle for 48 hours. At least two transects of the chamber bottom were observed with an inverted microscope [4] at 312 X magnification to enumerate the most frequent, generally smaller, phytoplankton forms. Additionally, the whole chamber bottom was examined at 125 X magnification to count the larger, less frequent cells. In both cases, all cells encountered were tallied. | Inverted microscope 125X magnification |
| Microbial cellular abundance growth response through epifluorescent microscopy from the Neuse River Estuary, North Carolina USA from 2021-2022 | Nikon Ti2 inverted microscope with excitation filters for: DAPI (395/25 nm), SYBR (470/40 nm), and autofloresence (620/60 nm). | Nikon Ti2 inverted microscope |
| Microscopy counts (Beggiatoa-like filaments, Cable bacteria), together with in situ temperature and salinity and surface sediment chlorophyll concentrations, of ex situ sediment cores collected in the Chesapeake Bay during 2017-2018 | Zeiss AxioVert A1 | |
| Microzooplankton abundance from phyto and microzooplankton experiments from the RVIB Nathaniel B. Palmer NBP0601 cruise in the Ross Sea, Southern Ocean from 2005-2006 (CORSACS project, Antarctic microzooplankton project) | Samples were enumerated using light microscopy at 200x magnification. A Zeiss microscope, model Axiovert S100 was used. | Inverted Microscope |
| Abundance results from microzooplankton experiments on the R/V Seward Johnson SJ0516 cruise between Ireland and Iceland during 2005, North Atlantic Spring Bloom (NASB 2005 project, Antarctic microzooplankton project) | /*-->*/ Counts were made using an inverted Zeiss Axiovert S100 microscope at 200× magnification (Utermohl 1958). | Inverted Microscope |
| Cell abundance estimates of heterotrophic protists by size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project) | Slides were digitally imaged using a Zeiss Axiovert 200 M inverted compound microscope equipped for high-throughput epifluorescence microscopy with a motorized focus drive, stage, objective and filters. | Zeiss Axiovert 200 M inverted compound microscope |
| Carbon biomass estimates of heterotrophic protists by size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project) | Slides were digitally imaged using a Zeiss Axiovert 200 M inverted compound microscope equipped for high-throughput epifluorescence microscopy with a motorized focus drive, stage, objective and filters. | Zeiss Axiovert 200 M inverted compound microscope |
| Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) location information on samples obtained on Gould (LMG1411) in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project) | Used to perform isolations | Olympus CKX41 |
| Group II Syndiniales infected host and dinospore counts determined from CARD-FISH hybridization carried out on samples collected at the Martha's Vineyard Coastal Observatory (MVCO) monthly or bimonthly from September 2019 to October 2020 | Hybridized filters were counted on a Zeiss Axioskop S-100 with epifluorescence. | Zeiss Axioskop S-100 |
| Lab experiment to test effects of live coral from Porites lobata, Pocillopora sp., Porites rus, and Millepora on Caerasignum maximum larvae after 24 hours. | Tubs were maintained in a flowthrough seawater table and examined after 24 h under a dissecting microscope. | dissecting microscope |
| Lab experiment to test effects of short-term exposure to live coral from corals, Porites lobata, Pocillopora sp., Porites rus, on Caerasignum maximum larvae (Vermetids_Corals project) | Tubs were maintained in a flowthrough seawater table and examined after 24 h under a dissecting microscope. | dissecting microscope |
| Cell abundance estimates of eukaryotic phytoplankton by taxa and size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project) | Slides were digitally imaged using a Zeiss Axiovert 200 M inverted compound microscope equipped for high-throughput epifluorescence microscopy with a motorized focus drive, stage, objective and filters. | Zeiss Axiovert 200 M inverted compound microscope |
| Carbon biomass estimates of eukaryotic phytoplankton by taxa and size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project) | Slides were digitally imaged using a Zeiss Axiovert 200 M inverted compound microscope equipped for high-throughput epifluorescence microscopy with a motorized focus drive, stage, objective and filters. | Zeiss Axiovert 200 M inverted compound microscope |
| Presence and absence of iron and light-related functional genes collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project) | Used to perform isolations | Olympus CKX41 |
| Protist carbon from microscopy samples collected in the Gulf of Mexico on R/V Nancy Foster cruises in May 2017 and May 2018 | Zeiss Axiovert 200M inverted compound microscopy | |
| Microzooplankton biomass estimates from PUA (polyunsaturated aldehydes) experiments, Virginia Coastal Bays and Bay of Napoli, Mar-July 2015 | The microscope was equipped with differential interference contrast (DIC), epifluorescence, and a digital camera. Biomass estimates for microzooplankton were determined after counting cells on an inverted microscope and converting volume estimates, from measurements with a reticle in the objective lens, to carbon concentrations using known conversion factors. | Olympus IX-70 inverted microscope |
| Plankton cell abundances and APA data from RV Atlantic Explorer BATS cruise BV50 in the North Atlantic subtropical gyre during September 2015. | Used in microscopy analyses | Nikon Diaphot inverted compound microscope |
| NCBI project accession and library information on each sample analyzed in upwelling experiments conducted on two phytoplankton species isolated from the California Upwelling Zone | Cells were enumerated using a Sedgwick-Rafter counting chamber on an Olympus CKX41 inverted microscope. | Olympus CKX41 inverted microscope |
| Aggregation of Thalassiosira weissflogii as a function of pCO2, temperature, and bacteria - Aggregation Phase - Carbonate System + TEP from UCSB MSI Passow Lab from 2009 to 2010 (OA - Ocean Acidification and Aggregation project) | Diatom cell abundance was monitored daily by counting cells in a Sedgwick-Rafter Cell S50 (SPI Supplies, West Chester, PA, USA) using an inverted Axiovert 200 microscope (Zeiss, Jena, Germany). | Inverted Axiovert 200 Microscope |
| Aggregation of Thalassiosira weissflogii as a function of pCO2, temperature and bacteria - Aggregation Phase - Sinking Velocity from a from 2009 to 2010 (OA - Ocean Acidification and Aggregation project) | Diatom cell abundance was monitored daily by counting cells in a Sedgwick-Rafter Cell S50 (SPI Supplies, West Chester, PA, USA) using an inverted Axiovert 200 microscope (Zeiss, Jena, Germany). | Inverted Axiovert 200 Microscope |
| Shotgun Proteomics of Pseudonitzschia multiseries Multi stress incubations. | Olympus CKX 41 inverted microscope | |
| Temperature and nutrient dependent phytoplankton growth and herbivorous protist grazing rates from the Long-term Plankton Time Series site in Narragansett Bay, RI in 2017 | Nikon Diaphot 300 | |
| Transcriptome statistics from samples obtained on LMG1411 collected on the Gould (LMG1411) in the Western Antarctica Peninsula in 2014. (Polar Transcriptomes project) | Used to perform isolations | Olympus CKX41 |
| Discrete raw measurements from upwelling experiments conducted on two phytoplankton species isolated from the California Upwelling Zone | Cells were enumerated using a Sedgwick-Rafter counting chamber on an Olympus CKX41 inverted microscope. | Olympus CKX41 inverted microscope |
| Eukaryotic phytoplankton abundance and composition from nitrate and vitamin-B enriched treatments, from up-welled coastal waters off Southern California, March 2015 (B-vitamin plankton succession project) | Used for cell counts: Samples of 50 ml volume were collected from each replicate of six treatments and preserved at 4°C in the dark with the addition of acidified Lugol’s solution an enumerated using an Accu-Scope 3032 inverted microscope. | Accu-Scope 3032 inverted microscope |