PlantCV
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Documentation
Installation
Updating PlantCV
Frequently Asked Questions
Analysis Approaches
Using Jupyter Notebooks
Summary of Output Measurements
Contributing
Contributing to PlantCV
Code of Conduct
Adding/Editing Documentation
Pull Request Review Process
Tutorials
Workflow Parallelization
Exporting Data
PlantCV Namespace
PlantCV
Inputs and Outputs
Print Image
Plot Image
Read Image
Read Bayer Raw Image
Analysis Methods
Analyze Color
Analyze Pixel Distributions
Analyze Grayscale
Analyze Size and Shape
Horizontal Boundary Tool
Vertical Boundary Tool
Analyze Thermal
Analyze Spectral Reflectance
Analyze Spectral Index
Analyze YII
Analyze NPQ
Annotation Tools
Points
Apply Mask
Auto Crop
Background Subtraction
Canny Edge Detection
Closing
Color Palette
Colorspace Conversion
RGB to Gray
RGB to CMYK
RGB to LAB
RGB to HSV
Create Labels
Crop
Crop and Position Mask
Dilation
Distance Transform
Erosion
Fill Objects
Fill Holes
Flood Fill
Flip Image
Filters
Eccentricity Filter
Laplace Filter
Sobel Filter
Scharr Filter
Gaussian Blur
Get Kernel
Histogram Normalization
Hyperspectral Data
Analyze Spectral Reflectance
Analyze Spectral Index
Calibrate HSI
Crop HSI
Spectral Index
Extract wavelength
Rotate HSI
Spectral data objects
Write HSI data
Image Add
Image Subtract
Image Fusion
Invert
I/O Functions
Random Subset
Read Dataset
Kmeans Clustering Classifier
Landmark Analysis
Acute
Space
StarScape
Constella
ConstellaQC
x-Axis Pseudolandmarks
y-Axis Pseudolandmarks
Scale Features
Landmark Reference Point Distribution
Logical Operations
Logical Operations-And
Logical Operations-Or
Logical Operations-XOr
Median Blur
Morphology Functions
Analyze_stem
Check Cycles
Fill Segments
Find Branches
Find Tips
Prune
Segment Angles
Combine Segments
Segment Curvature
Segment Euclidean Length
Segment ID
Segment Insertion Angle
Segment Path Length
Segment Skeleton
Segment Sort
Segment Tangent Angle
Skeletonize
Naive Bayes Classifier
Objects Class
Opening
Output Mask
Outputs Class
Photosynthesis Functions
Read CropReporter Data
Reassign Frame Labels
Analyze YII
Analyze NPQ
Visualize chlorophyll Fluorescence
Params (Debugging)
Print Image
Plot Image
Read Image
Read Bayer Raw Image
Report Size Marker
Region of Interest Tools
Create a Circular ROI
Create an Elliptical ROI
Create a Rectangular ROI
Create a Custom ROI
Create ROI from Binary Image
Create Multi ROIs
Create Grid of ROIs Automatically
Filter a mask by ROI
Filter a mask by ROI (quickly)
Convert ROI to Mask
Segment Image Series
Shift Image
Spatial Clustering
Spectral Index
Standard Deviation Filter
Thresholding Methods
Binary Threshold
Custom Range Threshold
Gaussian Adaptive Threshold
Mask Bad Threshold
Mean Adaptive Threshold
Otsu Auto Threshold
Saturation Threshold
Threshold Two Channels
Triangle Auto Threshold
Texture Threshold
Transformation Methods
Auto-Detect Color Card
Auto-Detect Color Card (old)
Calibrate Camera
Checkerboard Calibration
Create Color Card Mask
Convert Color Card to Matrix
Color Correction Workflow
Quick Color Check
Affine Color Correction
Standard Color Matrix
Gamma Correction
Merge Images
Nonuniform Illumination Correction
Perspective warp
Rescale Image Values
Resize Images
Rotate
Transformation Helpers
Calculate Moore-Penrose Inverse Matrix
Create Color Correction Matrix
Apply Color Correction Matrix
Load Matrix
Save Matrix
Visualization Methods
Auto Threshold Methods
Chlorophyll Fluorescence
Colorize Label Image
Colorize Masks
Colorspaces
Histogram
Hyperspectral Histogram
Overlay Images
Object Size ECDF
Object Sizes
Pixel Scatter Plot
Pseudocolor
Time Lapse Video
Watershed Segmentation
White balance
Within Frame
Machine Learning Training
Kmeans Clustering
Naive Bayes
Naive Bayes Multiclass
Parallelization
Configure Parallelization
Workflow Inputs Management
Metadata Parser
Job Builder
Multiprocess
Process Results
Workflow Parallelization
Accessory tools
PlantCV
psII tutorial
Edit on GitHub
Tutorial: Photosystem II Analysis, Single Plant
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Check out our interactive PSII tutorial!
Check out our interactive PSII tutorial! Check out our interactive PSII tutorial!