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Introduction to ImageJ
tutorial version 0.1.3
Research Computing Services
Tutorial Outline
Image Format Types
Raster Images
Raster Image Quality
Getting Started with ImageJ
Opening and saving images
Selections and cropping
Image Adjustments
Macros
Recording and running
Writing your own
Measurements
Area and dimensions
Histograms
ROI and masking
Thresholding
Quantification of intensity
Raster Image Files
Raster image files are composed of a grid of pixels.
Each pixel contains color or intensity information
File formats support many types of raster image
24 bit full color – RGB (8 bits per color) – png, tiff, rgb, bmp, jpg, jp2
32 bit full color with alpha – png, tiff, rgb, bmp, jpg, jp2
8 bit color map – gif, tiff, rgb
Bitmap (black and white only) – tiff, bmp.
Grayscale – can be 8,16, or 24-bit – png, tiff, bmp, jpg, jp2
24-bit RGB
8 bits each color at each pixel
Bits
The number of bits determines the number of intensity levels that can be digitally
encoded.
For non-power-of-two bits per pixel the image is usually stored in the next higher-up pixel
format.
Example: 10-bit image stored as a 16-bit TIFF. Only values 0-1023 would be used.
# of bits per pixel
(N)
Range of intensity
levels
(0 2
N
-1)
Image Type Computer
Representation
(C types)
8 0 - 255 grayscale
unsigned char (8 bits)
10 0 - 1023 grayscale
unsigned short (16 bits)
12 0 - 4095 grayscale
unsigned short (16 bits)
16 0 - 65,535 grayscale
unsigned short (16 bits)
24 0 – 16,777,215 grayscale
unsigned
int (32 bits)
3 x 8 0 - 255 per channel RGB
unsigned
int (32 bits)
4 x 8 0 - 255 per channel RGB with alpha
unsigned
int (32 bits)
What sets the # of bits and pixels?
The physical device capturing the image sets the number of pixels
The electronics that convert light intensity to an electronic signal sets the number of bits.
The image as
projected onto
the CCD chip.
Pixel (spatial)
resolution set when
chip is manufactured.
Charge accumulates
per pixel during
exposure.
Charge levels are read out
by a digitizer with a fixed
number of bits per pixel.
Charge levels over the
maximum bit value are
saturated.
232
209
187
206
172
119
155
178
234
198
162
195
255
222
188
245
8-bit digitization assigns the
values shown.
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