Image Processing Using ImageJ

Norbert Vischer

Centre for Advanced MicroscopyUniversity of Amsterdam

Image processing Image AnalysisData Organization

From Images to Results

Full well capacity:15 000 electrons

Image as a matrix

4 MP camera:

1 MPixel red2 MPixel green1 MPixel blue

4 MP color image

4 MPixel red4 MPixel green4 MPixel blue

Missing fields are interpolated

Color images

File types

TIFF (Tag Image File Format) : 8-bit 16 bit, 32bit, RGB,

uncompressed in ImageJ

JPEG / JFIF: Lossy Compression, 1:25

GIF (Graphics Interchange Format) : 8 bit Graphics, Animation,

lossless

PNG (Portable Network Graphics): RGB Graphics, Transparency,

lossless, superior to GIF, for screenshots

DICOM

FITS

File types

- 8 Bit- 16 Bit- RGB color-32 Bit Floating point----------------------------- (Hyper-)Stacks- Metadata- Spatial calibration-Density calibration

- Only uncompressed TIFF in ImageJ

TIFF is the most versatile format

TIFF: A File system within a file

JPEG Compression / Decompression

JPEG Artifacts

8 * 8 cell

Bit depth of image types