What is a digital image ? 1

Illustrator/Inkscape Bitmap/raster Vector Array of points (pixels) Not scalable (aliasing) Mathematical/geometric equations Scalable Microscopy Images Photoshop/GIMP ImageJ Illustrator/Inkscape Acrobat 2

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Y X RGB 24-bits Red 8-bits Green Blue 4 238 176 200 94 187 220 78 121 147 4

Microscope bitmap image A matrix of numbers Each number representing light intensity at a particular coordinate in the plane Pixel depth : the size and structure of the pixel intensity range Color is provided by the look-up table Additional data : what, where, when, how ? = metadata 5

Bit depth The sample signal intensity (infinite number of steps) is converted to pixel values (limited number of steps) by the sensor. 8-bit : from 0 to 255 (28=256 steps) 12-bit : from 0 to 4095 (212=4096 steps) 16-bit : from 0 to 65535 (216=65536 steps) RGB : three 8-bit grayscale channels for red, green and blue Hands-on : http://micro.magnet.fsu.edu/primer/java/digitalimaging/processing/bitdepth/index.html 6

16 bit 8 bit

16 bit 8 bit

Colour Monochrome CCD cameras and confocal photomultipliers (PMT) do not “see” colour. CCD sensor and PMT detect photons independently of their wavelengths (within their detection range). The wavelengths detected depend on the filter set installed inside the microscope Colour is false except for colour camera (RGB filter)

Look-up table (LUT) 255 10

Color is provided by the look-up table, color is always false RGB Red Green Blue Color is provided by the look-up table, color is always false 11

Histogram : pixel intensity distribution 12

Histogram : pixels distribution distribution of pixels intensity (x axis) plotted against the number of pixel (Y axis) independently of their localisation within the picture fill the dynamic range during image acquisition (black offset, saturation) 13

RGB Red Green Blue 860 x 860 pixels RGB color 8-bits per channel 14

Many images formats … Microscope specific formats GIF, TIF, BMP, PNG, ICS, JPEG, MPEG, Quicktime, SWF, PICT, EPS, PDF, PSD, XCF, … Microscope specific formats LIF, LEI, LSM, ZVI, STK, OIF, dv, r3d, PIC, IPL, OIB, OIF, ND2 15

Which format to use ? TIF (TIFF and variants) Loss-less compression (not always available) Suitable bit-depth Space for meta-data (scaling, exposure, …) Open Pretty much universal : should be readable in years from now Most image acquisition softwares have proprietary formats exportable as TIFF 16

Compression Loss-less compression Writes EXACTLY the same data in a smaller file ZIP Not that efficient (space/time) for microscopy data Lossy compression Change the dataset during compression JPEG NEVER USE for scientific data acquisition/analysis Good for web publication and pictures distribution 17

Metadata Excitation wavelength Emission wavelength Dyes Exposure Gain Offset Time interval Z-stack Optical slice thickness Objectives Pixel size : scale bar Personal notes … Use the proprietary file format or tiff format to save the essential metadata (6 months later what is that picture ?!?!?) 18

Digital Image Data Metadata array of pixels each pixel has an intensity value Metadata How, What, Where, When, Who… 19

Data Table of intensity value Picture formed of pixels of different intensity Histogram of pixel intensity distribution (loss of spatial information) 20