An image is a two-dimensional representation of visual information. It is an array of pixels, where each pixel represents a specific color and intensity. In digital images, the pixels are stored as numerical values in a computer-readable format.

Images have several properties that describe their characteristics, including:

  • Resolution: The number of pixels per inch or per centimeter (i.e. pixel size, e.g., most microscopy cameras have pixel sizes of 65 to 280 nm).
  • Bit depth: The number of bits used to represent each pixel (8-, 16-, 32-bit format). This determines the number of different shades of color that can be represented.
  • Color model: The system used to represent colors in the image, such as RGB (red, green, blue) or HSL (hue, saturation, lightness).
  • Compression: The method used to reduce the size of the image file, if any.

Images can contain different types of information, including:

  • Visual information such as color, texture, and shape of objects within the image.
  • Metadata such as the date and time the image was captured, camera settings, and light-source.

There are many different file formats for images, each with its own strengths and weaknesses. Some of the most common image file formats include:

  • JPEG: A lossy format that is widely used for photographic images.
  • PNG: A lossless format that supports transparency and is often used for graphics.
  • GIF: An older format that supports animation and a limited number of colors.
  • BMP: An uncompressed format that is widely supported, but can produce large files.
  • TIFF: A flexible format that can be either lossless or lossy and supports multiple images in a single file

Some other formats are DICOM, NIfTI, HDF5 for medical imaging, OME-TIFF for microscopy and bioimage analysis .


The difference between raw and processed images refers to the level of processing that the image has undergone.

Raw images are unmodified images that are directly captured from the imaging instrument, such as a microscope or a camera. These images typically contain a large amount of noise and artifacts, such as uneven illumination and distortion. Raw images also often have a high dynamic range, which can make it difficult to visualize fine details or make quantitative measurements.

Processed images, on the other hand, have been through some form of computational analysis or manipulation to improve their quality and/or to extract specific information. This process may include things like

  • Image preprocessing: such as denoising, background subtraction, intensity correction, and normalization
  • Segmentation: separating the image into regions of interest
  • Object detection and tracking
  • Measurement of morphological or other features of the objects
  • Statistical analysis

The goal of processing an image is to make it more suitable for further analysis, such as quantifying the number of cells in an image or measuring the fluorescence intensity of a protein.

Raw images are usually used as a reference for the original data and are important to preserve for later verification or reproducibility of the results. Processed images are used to observe and analyze the data to extract the information of interest.


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