Image formation and imaging artefacts course overview
To get reliable and quantifiable data, it is important to understand how an image is formed and what can be quantified depending on the image properties. The imaging process does not generate an exact representation of the “real” structure. For instance, small structures may not be distinguishable due to the instrinsic blur induced by a microscope (resolution limit), measured intensities may be affected by the position of an object in the field of view.
Prerequisites
Before starting this lesson, you should be familiar with:
Learning Objectives
After completing this lesson, learners should be able to:
Understand how an image is formed
Understand how artefacts affect the final image and the analysis
Understand how to mitigate imaging artefacts
Concept map
graph LR
%% 1. IMAGE FORMATION (Top Layer - LR)
subgraph Formation [Image Formation]
direction LR
Light[Light Source] --> Sample[Sample]
Sample --> Optics[Optics]
Optics --> Detector[Detector]
Detector --> Raw[Raw Image]
end
%% 2. ARTEFACTS (Bottom Layer - LR)
subgraph Artefacts [Artefacts]
direction LR
SampleAb["Bleaching
Refractive index mismatch
Labelling
..."] OptAb["Blur
Shading
Spherical
Chromatic
Crosstalk..."] DetAb["Sampling / Aliasing
Noise
Saturation
..."] %% Force LR order in the bottom row SampleAb ~~~ OptAb ~~~ DetAb end %% 3. CORRECTIONS (Right Layer - TB) subgraph Correction [Corrections] direction TB Raw --> Proc{Processing} Proc --> BC[Bleach Correction] Proc --> FFC[Flat-field Correction] Proc --> Decon[Deconvolution] Proc --> Pdot[...] BC & FFC & Decon & Pdot --> Final[Final Image] end %% POSITIONING CONSTRAINTS %% ASSOCIATIONS (Vertical lines linking stage to artifact) Light --- OptAb Light --- SampleAb Sample --- SampleAb Optics --- OptAb Detector --- DetAb %% Force Artefacts subgraph to start below Formation subgraph Light ~~~ SampleAb Sample ~~~ SampleAb Optics ~~~ OptAb Detector ~~~ DetAb %% STYLING classDef art fill:#fff1f1,stroke:#d63031,stroke-width:1px,stroke-dasharray: 5 5; classDef form fill:#f1fff1,stroke:#27ae60,stroke-width:2px; classDef corr fill:#f1f1ff,stroke:#0984e3,stroke-width:2px; %% Fixed case-sensitivity for OptAb class SampleAb,OptAb,DetAb art; class Light,Sample,Optics,Detector,Raw form; class Proc,BC,FFC,Decon,Final corr;
Refractive index mismatch
Labelling
..."] OptAb["Blur
Shading
Spherical
Chromatic
Crosstalk..."] DetAb["Sampling / Aliasing
Noise
Saturation
..."] %% Force LR order in the bottom row SampleAb ~~~ OptAb ~~~ DetAb end %% 3. CORRECTIONS (Right Layer - TB) subgraph Correction [Corrections] direction TB Raw --> Proc{Processing} Proc --> BC[Bleach Correction] Proc --> FFC[Flat-field Correction] Proc --> Decon[Deconvolution] Proc --> Pdot[...] BC & FFC & Decon & Pdot --> Final[Final Image] end %% POSITIONING CONSTRAINTS %% ASSOCIATIONS (Vertical lines linking stage to artifact) Light --- OptAb Light --- SampleAb Sample --- SampleAb Optics --- OptAb Detector --- DetAb %% Force Artefacts subgraph to start below Formation subgraph Light ~~~ SampleAb Sample ~~~ SampleAb Optics ~~~ OptAb Detector ~~~ DetAb %% STYLING classDef art fill:#fff1f1,stroke:#d63031,stroke-width:1px,stroke-dasharray: 5 5; classDef form fill:#f1fff1,stroke:#27ae60,stroke-width:2px; classDef corr fill:#f1f1ff,stroke:#0984e3,stroke-width:2px; %% Fixed case-sensitivity for OptAb class SampleAb,OptAb,DetAb art; class Light,Sample,Optics,Detector,Raw form; class Proc,BC,FFC,Decon,Final corr;
Figure
Follow-up material
Recommended follow-up modules:
Learn more: