A 35–37°C incubator is essential for culturing pathogens on both solid and liquid media. This incubator should have a microprocessor to allow for a constant infusion of 3% to 5% carbon dioxide. Some pathogens, particularly Neisseria species, require higher amounts of carbon dioxide. Such bacteria can be cultured in the same incubator by using special media and sodium bicarbonate or a candle jar.

The incubator should also have a stainless steel tray of autoclaved, distilled water to maintain humidity. Without additional humidity, water evaporation from the media will occur. However, it is easy for this water to become a breeding ground for contamination. The stainless steel tray should be cleaned with bleach regularly, and only autoclaved water should be used to fill the tray.

A complete ocular microbiology lab includes anaerobic incubators. These are usually tight-sealing, carbon dioxide-filled jars held at room temperature.

A 30°C incubator can be used for fungal and certain bacterial cultures. However, fungal cultures can be performed at room temperature and only rare bacteria grow at 30°C.

There are two types of hoods present in the ocular microbiology lab. The first type is a chemical hood for hazardous chemicals. This hood has both air flow and exhaust systems, and the sash provides mechanical protection to the user. The other type of hood is the biological safety cabinet (BSC), which protects the workspace to limit aerosol exposure to infectious materials. The class I BSC has airflow and exhaust systems similar to the fume hood, but additionally, the exhaust is sent through a HEPA filter that can remove up to femtometer-sized particles.

The class II BSC has the added feature of a downward laminar flow of HEPA-filtered air, so that only filtered air flows over the materials in the hood. This decreases cross-contamination along the work surface, and makes class II BSCs more useful. Both types of BSCs are usually fitted with a UV light connected to a timer that can also be used to disinfect the cabinet. Ideally, gas, vacuum, air, and water taps are fitted inside the hood.

Corrosive and flammable materials must be kept in appropriate cabinets with secondary containment. Chemicals that will react with each other, such as sodium hydroxide and sulfuric hydroxide, should not be stored in proximity.

Given the range of protocols used by an ocular microbiology laboratory, multiple sizes of centrifuges are used. Tabletop microcentrifuges are the workhorse of an ocular microbiology laboratory. Given the small sizes of ocular samples, the microcentrifuge is used to both concentrate samples and pellet debris. A medium-sized centrifuge, capable of holding 15 mL, 50 mL, and standard blood tubes, is also necessary for larger sample preparation. A cytospin centrifuge prepares slides from cells in solution, and is an invaluable tool in preparing cytologic studies of aqueous and vitreous fluid samples. Ultracentrifuges are generally not required for the ocular microbiology laboratory.

Bunsen burners are primarily used to sterilize wire or glass inoculation loops, and flame the neck of media bottles in aseptic technique. The flame can also be used to heat-fix samples on microscope slides. Slides, samples, and solutions can also be heated on electric heat blocks with digital control of temperature. These often have a magnetic stir function incorporated into the base. Hot water baths set at 37°C are useful for thawing frozen solutions and for warming media.

Multiple types of spark-arrested refrigerators and freezers are needed as different samples and compounds are stable at varying temperatures. Many chemicals and molecular biology kits can be stored at room temperature. A refrigerator at 4°C to 8°C is used for long-term storage of bacterial media and short-term shortage of ocular specimens or purified DNA. The refrigerator should be clean and have sufficient space to keep new media away from infectious samples.

Two types of freezers are necessary: one at -20°C and one at -80°C. Most DNA, enzymes, and antibodies are stable at -20°C for over 6 months but will keep even longer at -80°C. Multiple freeze–thaw cycles will cause deterioration of a sample and should be avoided.

The -80°C freezer is necessary for archiving patient samples, DNA, and stocks of solutions. A liquid nitrogen Dewar flask is used for cryogenic freezing and storage of cell culture stocks at -197°C. Such flasks are usually available as common equipment shared between laboratories.

Microscopy is used for both the detection of pathogens in a sample and for characterizing organisms grown in culture. A binocular microscope using a tungsten light source is essential. The eyepiece of this scope provides 10× magnification; objective lenses magnify at 5×, 10×, 20×, and 40×. Usually, a 100× objective is provided for oil immersion. Even higher magnification objectives can be used for phase contrast microscopy, where unstained organisms and particles can be visualized. This is particularly useful for examining contact and intraocular lenses. Attachments for fluorescent imaging increase the usefulness of the microscope. If possible, the microscope should be linked to a digital camera for recording images. These images can then be enhanced using appropriate software, and then archived for educational and publication purposes.

Confocal microscopes are useful for research studies, but are not commonly used to identify pathogens. Dark-field microscopy is used for detection of spirochetes. Electron microscopes are rarely used to characterize pathogens, and usually found in a research core lab.

Molecular protocols for diagnosis of infection are increasingly complementing traditional culture methods. The polymerase chain reaction (PCR) is the major technique used for pathogen DNA detection. PCR is typically performed using a programmable thermal cycler. These machines are programmed to raise and lower the temperature for each step of the PCR. PCR products are generally analyzed by electrophoresis on polyacrylamide or agarose gels. Real-time thermocyclers can generate more quantitative results and obviate the need for electrophoresis. Preparing PCR samples in an airflow cabinet (PCR hood) fitted with UV lights in a room remote from the thermocycler can reduce contamination.