biovoxxel
Scientific Image Editing and Figure Creation
Introduction
Introduction
Course Preparation
Fiji Installation and Configuration
Inkscape Installation
Exercise Image Download and General Info
Introductions to the Fiji User Interface (GUI)
Basic Image Handling in Fiji (for Beginners)
Working with Digital Scientific Images
Scientific Image File Formats and Their Handling
Behind the Scenes - Image Metadata
Image Scaling (important!) - With and without Metadata
Intensity versus Color - Important Distinction
Pseudo Colors
Human Perception and Display
Lookup Tables, Pseuso-/False-Colors
Image Editing
Introduction to Image Editing
Image Illumination Correction
Introduction to Uneven Illumination Correction
Quantitative and Qualitative Illumination Correction
Unspecific Signal Reduction
Unspecific Signal Reduction (for fluorescence images)
Contrast Adjustment
Introduction to Contrast
Grayscale Contrast Adjustment
Color/RGB Contrast Adjustment
Avoid Gamma Adjustment!
Channel Merging
Channel Merging in Fiji
Labeling 2D Images in Fiji
Adding a Scale Bar
Adding Arrows and ROIs to the Image Overlay
Exporting Images for Figures
Difference Bitmap vs. Vector Graphic - Exporting SVGs
Image Transformations (Size & Rotation)
Don't Change your Data (Problems with Image Transformation)
Proper Inset/Zoom Creation
3D Time Data in Publications
Time Stamping Movies
Creating and Labelling of Kymographs
3D Volumetric Data in Publications
Options and Limitations
Orthogonal Views
Z Projections
3D Reconstruction - Basics using the 3Dscript plugin
Setting up Inkscape
The Inkscape User Interface
Basic Handling of Inkscape
Installing Inkscape Extensions
Creating Figure Panels with Inkscape
Importing and Handling Images in Inkscape
Manual Image Alignment
Automatic Image Alignments in Grids
Batch Adapt Multiple Objects at Once
Creating Image Clips ("Crops")
Labelling Figures in Inkscape
Adding Labels to Panels
Adding and Modifying Data Plots
Adding Data Plots to Inkscape
Exporting Figures
Save Figures and Figure Parts in Different Formats
Bonus - 3D Animations with 3DScript
3D Animations in 3Dscript
4D Animation in 3Dscript and Saving Movies
Bonus - Tipps for Poster preparation in Inkscape
Tips for Poster Templates and QR-Code Generation in Inkscape
Summary DO's and DON'ts in Publication Figures
DO's and DON'ts
Wrap-Up and Certificate
Scientific Image Editing and Figure Creation
Adding Data Plots to Inkscape