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Knowledge book - Image processing and analysis - : - Coggle Diagram
Knowledge book
- Image processing and analysis -
:
Topic
Image DATA Management
Sequence
DMP
Sequence
Using OPIDOR
Sequence
Using DSW
Sequence
DMP structure v DMP project
Sequence
Publishing /archiving in repository
Sequence
Image format
Sequence
using an image database
Topic
What is a numerical image ?
Sequence
Pixel vs voxel
Sequence obligatoire
Sequence
What is a file format ?
Sequence obligatoire
Sequence
What is bit-depth ?
Sequence obligatoire
Topic
Working with color images and images in color
Sequence
RGB images
Sequence
Hyperstack
Sequence
Spatial sampling
Sequence
Metadata
Field
Pipelines
Topic
Machine Learning
Network architecture
GANs
random forest/SVM
Sequence
deep learning
convolutional filters
convolutional networks
Features
metrics, loss function
Generating the training dataset
Annotating the data
Data augmentation
Topic
Stitching/registration
Similarity metrics
Interpolation
Transformation basis
Optimization
Stuck in a local minima
Extracting fiducials
Topic
Restoration
Sequence
Denoising :
Filtering
Restoration assessment
Deconvolution
Algorithms
Regularization
Reference: PSF/IRF
Metrics
Automation
macros
Topic
Recording simple macros for batch processing; from workflows to macros
Sequence
ImageJ language discovery (functions / variables / operators)
Sequence
Advanced macro concepts (if / for / Dialogs)
Sequence
Intro Macro (concept / interest)
Sequence
Essential tools (MacroRecorder / Batch / built-in macro fonctions repository)
Topic
Colocalisation
Object-based methods
Coïncidence of pixels (thresholded Manders)
Coïncidence of features (volume-volume, volume-center...)
Distance-based methods
Intensity-based methods
Correlation- based (Pearson, Spearman)
Coïncidence of intensities (Manders)
Line-scan/Profiles method
Cross-correlation function (Van Steensel)
Interpreting the data
Transformations to generate control data
Randomization to generate control data
Field
Analyzing dynamics
Topic
Tracking/SPT
Kymographs
Cost function
Detection methods
Parameters extraction/Metrics
Choosing the right parameters (lasers, ROI etc...) ==> Link to photonics
Corrections
Data fitting/Modelling
Image registration
Normalization
Field
Visualization
Shaping figures
Topic
Assembling data for publication
Sequence
Reminder Adjust B&C
Sequence
Look up tables
Sequence
Scale Bar
Sequence
Text tool & Stack Label
Sequence
Make Montage / Figure J
Topic
Working with stacks: 3D Image Visualisation
Sequence
Simple visualisation
Sequence
Orthogonal views
Sequence
2D projections
Sequence
3D projections
Sequence
Ray tracing (3D viewer)
Application
Alternative software for 3D viewing: freeware (ex: Drishti), commercial (ex: Amira/Imaris/Arivis)
Application
Visualizing Big Data
Sequence
Different types of 3D data: 3D stacks vs tomograms
Field
Quantifications
Topic
Feature measurements
Sequence
Background's pixels vs Object's pixels: the notion of segmentation
Sequence
Grouping pixels into objects: connexity analysis
Sequence
Extracting numerical values from objects: how to measure perimeter, area, volume
Sequence
Notion of Region of Interest
Sequence
Performing simple measurement from ROIs using ImageJ (set measurements/measure)
Sequence
Automatically caracterizing objects in 2D using ImageJ
Sequence
Automatically caracterizing objects in 3D using ImageJ
Sequence
Image calibration (Set Sale / Metadata exploration / Pix size calculation)
Topic
Object detection
Sequence
Simplest way to differentiate Background's pixels vs Object's pixels: thresholding, and its limitations
Sequence
Grouping pixels into objects: connexity analysis
Sequence
How it works/how to use: the magic wand
Sequence
More advanced topic: active contours
Sequence
Histogram segmentation
Sequence
Working on point-like structures: detection of local maxima
Sequence
Background's pixels vs Object's pixels: the notion of segmentation
Field
Image processing
Topic
Filters
Sequence
Frequency filtering
Sequence
Image/Image operations
Sequence
Spatial filtering: Linear filters
Sequence
Spatial filtering: adaptative filters
Sequence
Coupling filtering and detection: wavelets
Sequence
Spatial filtering: non linear filters
Topic
Histogram manipulation
What is the histogram
Linear manipulation
Non linear manipulation
Morphomaths
Sequence
Boolean operations with masks
Sequence
Dilation/erosion
Sequence
Open/close
Sequence
EDM/UEP/Watershed/Skeleton/Voronoi
Sequence
Fill holes
Sequence
Logical operations between masks
Field
Ethics
Topic
Ethics in Image Processing
Sequence
Histogram manipulations
Sequence
Guidelines on figures
Checking and preserving the quantitative intensity content of your images
Topic
Quality assessment
SNR estimation
From metadata
SBR estimation
Resolution estimation
Error map