Laboratory Imaging & Photography

Michael Peres is the editor-in-chief of The Focal Encyclopedia of Photography, 4th Edition, and former chair of the biomedical photographic communications department at the Rochester Institute of Technology. Since 1986, he has taught photomicrography, biomedical photography and other applications of photography used in science. Prior to joining the RIT faculty, Peres worked at Henry Ford Hospital and the Charleston Division of West Virginia University as a medical photographer. He is the recipient of the RIT Eisenhart Outstanding Teaching Award and the Schmidt Medal for Lifetime Achievement in the Field of Biocommunications.

• AcknowledgementsPreface: The BeginningIntroduction: The Imaging Chain Foundations, Fundamentals, Principles and Theory Chapter 1 Defining a Science ImageA Frame of Reference for the Image in ScienceThe Science Image: a point of departure Criteria for Good PhotographyScience Photographs require a ScalePhotographer’s Intent and Subject MatterA picture is worth a thousand wordsThe beginnings of permanent photographs and scientific photographyMaking the Invisible visibleHistorical images and Contemporary Point of ViewStandardized Approaches and RepeatabilityFather of Standardized ImagingInnovators and technological progressInstrumentationMicroscopy and Carl ZeissThe Invisible SpectrumAdvancement of Film Technology – Kodak. Agfa, Ilford and PolaroidShort Duration Light, Electric Flash and StroboscopesModern Technologies - Digital and Electronic PhotographyScanning Electron MicroscopyConfocal MicroscopeDuality of Images Science Images as ArtChapter 2 Human Vision and Perception The Human Visual SystemThe Imaging Room Seeing Basic Structure of the Human Visual SystemOptics of the Eye and Image Formation Physiology of SeeingDominant EyeVisual Perception and the Physiological of SightPerception of colorPersistence of VisionAfterimagePerception of DepthAdaptionMore on PerceptionIllusions Chapter 3 Applied Physics and Image Formation for the Scientific PhotographerVisibility requires Contrast, Magnification, and Resolution Light & IlluminationSources and SpectrumsContinuous and Discontinuous SpectrumsColor temperatureLight behaviours Reflection Refraction Dispersion InterferenceLensesLenses for Scientific ApplicationsFundamental opticsTeleconvertersWorking DistanceClose up LensesSupplementary LensesMirror LensesTelecentric LensesPhotographic FiltersPolarizing FiltersNeutral Density FiltersAberrationsCurvature of the FieldChromatic AberrationsDepth of FieldDiffraction Chapter 4 Digital Cameras, Digital Images, and Strategies The role of the cameraCamera ComponentsShuttersModes of OperationManualAutomaticSecondary Modes of OperationPhotographic ExposureLight measurementTypes of ShuttersFocal Plane ShuttersSyncing with electronic flashElectronic shuttersShutter affects on subjectsVibration affectsMirrorless camerasSensors PixelsSingle shot camerasScanning arraysMulti-shot arraysSensor sensitivity ISO, Binning, GainNoise production, dark, shot, sensor and evaluating Sensor evaluationBit depthColor spaceGammaWhite balanceSpectral sensitivityCapture file formatsOther file formatsFiltersSharpeningColor reproductionNoise reductionDigital ArtifactsConnecting devicesMemory cards Applications, Best Practices and Methods Chapter 5 The Sample and its Role in Laboratory PhotographyLaboratory Photography OverviewThe Sample and TreatmentTreatmentPreparationSelecting a SampleIsolating the sampleObjects and characteristicsIsolating the subject CompositionHandling samples, preparation and treatmentsStaining and other contrast producing factorsWet samples and immersion methodsMaking chambers Specimen TablesSurface replicasWhite, Black or Gray BackgroundsUse of Scales to indicate sizeChapter 6 Basic Laboratory Photography Methods: Close-Up Photography, Photomacrography, and StereomicroscopyOverview of Close-up PhotographyClose- Up MethodsLenses for Close-Up PhotographySupplementary LensesExtension Tubes Focusing, Depth of Field, and DiffractionCreating Camera to Subject AlignmentSelecting the ApertureExposure in Close-Up applications PhotomacrographyIntroductionBellows and Laboratory Set-UpsTrue Macro Lenses and Optical ConsiderationsOther lenses that can be used for magnifications 2:1 and higherSetting up a Macro SystemExposure CompensationExposure Factor equationsDepth of FieldStereo MicroscopesPhotographing with a stereomicroscopeChapter 7 Advanced Laboratory Photography Methods – Making Things VisibleIntroductionI- FluorescenceJablonski diagramUltraviolet and Short Wave Blue ExcitationThe Fluorescence SystemII - Photographing with the Invisible spectrum Basic ProblemsEnergy SourcesCamerasLensesFiltersFocusingLive View or Auto-focusExposure DeterminationIncreasing the ISONoise Reduction FiltersWork tetheredMultiple Discharges for Electronic FlashOther StrategiesIII - Polarized lightSeeing internal structureThe SystemIV - SchlierenPhotographing Schlieren Images V - Scanners as CamerasScanner SettingsUsing DescreenUnsharp MaskingImaging Objects on a ScannerVI - Peripheral PhotographyVII - Stereo and AnaglyphsMaking a Stereo PairMaking an AnaglyphVIII - StroboscopyChapter 8 A Primer for Lighting Small Laboratory SubjectsThere is light and then there is lightingMaking good light White and Neutral BackgroundsMaking ContrastReducing ContrastAxial lightingGlassware Metal and tent lightingImmersion methodsA Working SummaryChapter 9 Light Microscopy I - Foundations and brightfield methodsIntroductionFundamentals of Magnified Images Optical MagnificationOptical Elements on a Light MicroscopeEyepiecesPrismPhoto or Imaging System LensesSubstage CondendsersObjectivesNumerical ApertureForming Images - Diffraction and ResolutionMore on Numerical ApertureObjective CorrectionsFundamentals useful in Operating a Light MicroscopeSetting the EyepiecesFocusing Very Small Working DistancesInterpupillary DistancesLooking into the Body TubeNosepiece or TurretsAdjusting the Substage CondenserSetting the Field DiaphragmLampSetting the Aperture DiaphragmEstablishing Proper Brightfield or Kohler IlluminationMore on Kohler Photographing using a Light MicroscopeInstrument CamerasDSLR camerasAttaching a Camera to a MicroscopeII: Advanced Methods DarkfieldDifferential Interference ContrastFluorescence Phase ContrastPolarized lightRheinberg Differential Colorization TechniqueChapter 10 Confocal Microscopy by James Hayden IntroductionWhy Confocal ?Types of Confocal MicroscopesFluorescence Microscopy and Confocal MethodsFluorescent MarkersChoosing and Working with FluorophoresHow a Confocal Microscope Works Balance and Compromises required for forming a Good 2D imageHardware ConsiderationsLasersDetectorsOverview of Instruments Controls and SoftwareLaser PowerDetector SettingsSimultaneous of Sequential AcquisitionGain and OffsetPinhole Size and ResolutionSpatial Resolution and FormatScanning SpeedBidirectional ScanningDigital ZoomBit depthAveraging / Signal to NoiseAccumulation3D imagingConsiderations for Creating an Effective Z stackConsideration for Live Cell ImagingAdvanced techniquesChapter 11 Scanning Electron Microscopy by Ted KinsmanIntroductionHistoryModern Machines Theory and Design of InstrumentsThe Nature of an Electron in a VacuumElectron SourceElectron Microscopy OpticsAstigmatizationThe Electron ApertureResolution in a SEMSignal to Noise RatioScan Rotation Specimen Charging Maximizing ResolutionSample PreparationCritical Point DryingSputter CoatingChapter 12Ethical Considerations in Scientific Photography: Why Ethics? by James HaydenThe Need for ProtocolsThe Image as DataManipulation and DisclosureManipulation by Specimen SelectionManipulation by Hardware SettingsManipulation by Imaging TechniqueManipulation by SoftwareManipulation by PresentationForensic Examination Uncovering Digital Image FraudIndustry OversightConsequencesConclusionsChapter 13 Considerations and Methods for Image Processing in Science by Staffan LarssonIntroduction Terminology: Manipulation, Enhancement, Clarification SoftwareImage JGIMPAdobe PhotoshopBasic Color TheoryFundamental Digital Color ModelsChannelsLayersFundamental Image Editing Methods in ScienceMonitor CalibrationSelection tools and tools overviewImage SizeImage Editing Tools OverviewSelection Image editing toolsPixel Adjustment ToolsImage ProcessingI - Contrast and Color Balance CorrectionsMethod: Setting a white and black point Method: Changing contrast using LevelsMethod: Using CurvesII - Converting RGB files to Grayscale Method: GrayscaleMethod: Split ChannelsMethod: Channel MixerMethod: Black and White Adjustment LayerIII – SharpeningMethod: Unsharp MaskingMethod: High Band Pass FilterNoise reduction using Adobe Camera RAWMethod: Eliminating Luminance NoiseMethod: DespeckleMethod: Smart Blur FilterMethod: Reducing Noise using the Reduce Noise FilterV – Noise Reduction using the Camera Raw Convertor Software Method: Using the Camera RAW ModuleVI - Combining fluorescent imagesVII - Pseudo-coloring B & W imagesVIII - Making composite images Method: Making a Composite FileIX- Type and the Text ToolX - ShapesXI - Preparing files for PublicationMethod: converting RGB to CMYKMethod: Evaluating a CMYK images Black PointProfilesProofingGamut Warning Chapter 14 Applications of Computational Photography for Scientist PhotographersImage editing and Batch Processing Making actionsIncreased DOF Making Image SlicesGlobal Image Processing Z Stack file processing using Adobe® Photoshop Z Stack file processing using Helicon Focus® Z Stack file processing using Zerene Stacker Wide field high resolutionMethodsGlobal Image ProcessingCreating the Image MapHigh Dynamic Range ImagesMaking Photographic Exposures for HDR Blending the ImagesTime based imagingPhotographic ConsiderationsIntervalometersMaking the PhotographsChapter 15 Best Practices IntroductionMore Thoughts about Best Practices and WorkflowThe Laboratory and Environmental conditionsCleanliness is imperativeOptimizing Camera’s SettingsCleaning A Lens Monitors and video displaysColor ManagementSoftware, upgrades and Optimizing a ComputerImage Workflow, Folders, and Naming FilesArchiving, Data Redundancy, and Backing UpPlanning for Data loss and Disk Failure Digital housekeepingKeeping things Tuned UpSmart phone photographySocial MediaConclusionBest Practices Cheat Sheet

"The book is both comprehensive and accessible to photographers at all levels. Each topic is approached without expectation of previous knowledge from the reader or any photographic snobbery. For example, whether you are reading about comparisons between focal plane, sync speed, leaf and electronic shutters or how to apply an un-sharpen mask in Photoshop, everything is written in an easy-to-digest way for photographers of all backgrounds. [It] provides theoretical content to underpin many of the day-to-day practices of a medical photographer. Other practising clinical photographers will find the book reaffirms much of their current knowledge, while enhancing their understanding in some areas and potentially providing an introduction to unfamiliar techniques.The underlying feeling I had throughout reading this book was ‘why couldn’t this book have been available while I was studying?’ I will certainly be using the book as part of my continuing professional development for many years to come."—Simon Brinkworth, Medical Illustration, Marlborough Hill Workshops, Bristol, UK © 2018 The Institute of Medical Illustrators