Tools overview by category
Info
Some tools may be in more than one category
Ancillary
Tools mostly used inside other tools
Edge detectors
Performs edge detection with various common operators.
Mostly used by other tools.
Details here
Assert...
Assert something, returns wether or not assertion is passed
Assert mask position
Check that the mask intersects with a named ROI
Details here
Check source image
Checks image and returns error if something is wrong.
Details here
Clustering
Clustering tools
Felsenszwalb
From scikit-image: Computes Felsenszwalb’s efficient graph based image segmentation.
Details here
Quick shift
From scikit-image: Quick shift segments image using quickshift clustering in Color-(x,y) space.
Details here
Slic
From scikit-image: Segments image using k-means clustering in Color-(x,y,z) space.
Details here
Create an ROI
Create an ROI
Annulus ROI
Creates annulus ROIs
Details here
Circle ROI
Create circle ROIs
Details here
Hough circles detector
Hough circles detector: Perform a circular Hough transform.
Can generate ROIs
Details here
ROI composition
Create an ROI by composing other ROIs
Details here
ROI manager (deprecated)
Handles ROI edition via user input
Details here
Rectangle ROI
Create rectangle ROIs
Details here
Rotated rectangle ROI
Create rotated rectangle ROIs
Details here
Demo
Demo tools, start here if you want to understand how to create/edit tools
IPT Demo
IPT Demo (Image Processing Tool Demo)
A simple showcase of some of the available widgets
Best starting point if you want to build your own widgets
Details here
Execute default process
Execute a class pipeline linked to the selected image experiment, if no class pipeline is available an error will be reported
Default process
Performs the default process associated with the experiment.
If no default process is available, all channels will be printed.
Details here
Exposure fixing
Fix image exposure, the resulting image will be used for color analysis
Fix perspective
Fixes perspective using four dots to detect rectangle boundary.
Use the included threshold utility to detect the dots.
Details here
Image transformations
Performs various transformations on the image
Details here
Median Filter
'Apply median filter
Details here
Normalize Image
'Normalize image
Details here
Rotate
Rotates an image according to selected angle
Details here
Simple white balance
Simple white balance: Performs a simple white balance.
https://www.ipol.im/pub/art/2011/llmps-scb/article.pdf
Details here
Temperature and tint
Simple method to alter an image temperature and tint
http://www.tannerhelland.com/5675/simple-algorithms-adjusting-image-temperature-tint/
Details here
Feature extraction
Tools to extract features from a segmented image
Analyze bound
Analyses object bound.
Needs a mask as an input.
Normally used in a pipeline after a clean mask is created.
Details here
Analyze chlorophyll
Analyses chlorophyll data and returns mean and standard deviation
Details here
Analyze color
Analyses object color.
Needs a mask as an input.
Normally used in a pipeline after a clean mask is created.
Details here
Analyze object
Analyses object and returns morphologic data.
Needs a mask as an input.
Normally used in a pipeline after a clean mask is created.
Details here
Hough lines detector
Use the OpenCV functions HoughLines and HoughLinesP to detect lines in an image.
Details here
Image statistics
Displays image color statistics
Details here
Observation data
Returns observation data retrieved from the image file
Details here
Image generator
Creates one or more images from a selected image
Augment data
Copies image to target folder after modifying it
Can have a ROI as a pre-processor
Details here
Copy or rename image
Copies an image, renaming it if needed
Details here
Visualization helper
'With the current image and a mask build a visualization for selected features
Details here
Image info
Gives info about current image
Hough lines detector
Use the OpenCV functions HoughLines and HoughLinesP to detect lines in an image.
Details here
Mask cleanup
Cleans a coarse mask generated by threshold tools
Apply ROI
Apply selected ROI to image/mask
ROI can be of type "keep", "delete", "erode", "dilate", "open", "close"
Select correct IO type for pipeline use
Details here
Clean horizontal noise
Removes noise in the form of horizontal lines from masks.
Used with light barriers
Details here
Clean horizontal noise (Hough method)
Removes noise in the form of horizontal lines from masks using Hough transformation.
Used with light barriers
Details here
Fill mask holes
Fills holes in mask
Details here
Filter contour by size
'Keep or descard contours according to their size
Details here
Keep Biggest Contours
Keeps the contours inside the biggest one.
Needs to be part of a pipeline where a mask has already been generated
Details here
Keep countours near ROIs
Keep big contours inside a series of ROIs.
Small contours inside ROIs may be added on conditions.
Contours outsside ROIs may be added to root contours if close enough
Details here
Keep linked Contours
Keeps contours related to the main object, removes the others.
Needs to be part of a pipeline where a mask has already been generated
Details here
Morphology
Morphology: Applies the selected morphology operator.
Needs to be part of a pipeline where a mask has already been generated
Details here
Remove plant guide
Removes plant guide. Built for Heliasen light barrier
Details here
Skeletonize
Skeletonize: Thins the input mask to one pixel width lines.
Input needs to be a binary mask.
Details here
Pre processing
Transform the image to help segmentation, the image may not retain it's properties. Changes here will be ignored when extracting features
Apply ROI
Apply selected ROI to image/mask
ROI can be of type "keep", "delete", "erode", "dilate", "open", "close"
Select correct IO type for pipeline use
Details here
CLAHE
Contrast Limited Adaptive Histogram Equalization (CLAHE).
Equalizes image using multiple histograms
Details here
Channel mixer
Creates an new image by combining 3 channels from of the color spaces available.
Details here
Channel operation
Performs arithmetic operation between up to 3 channels
Details here
Channel subtraction
Creates a new channel by subtracting one channel to another.
Details here
Check exposure
Displays over/under exposed parts of the image
Also displays average brightness of the image
Details here
Crop
'Crop image or mask to rectangular ROI
Details here
Custom channels
Builds a mask or a channel by comparing pixels to the average value.
Details here
Edge detectors
Performs edge detection with various common operators.
Mostly used by other tools.
Details here
Filtering regional maxima
From scikit image - Filtering regional maxima: Perform a morphological reconstruction of an image.
Morphological reconstruction by dilation is similar to basic morphological dilation: high-intensity values willreplace nearby low-intensity values. The basic dilation operator, however, uses a structuring element todetermine how far a value in the input image can spread. In contrast, reconstruction uses two images: a "seed"image, which specifies the values that spread, and a "mask" image, which gives the maximum allowed value ateach pixel. The mask image, like the structuring element, limits the spread of high-intensity values.Reconstruction by erosion is simply the inverse: low-intensity values spread from the seed image and arelimited by the mask image, which represents the minimum allowed value.
Alternatively, you can think of reconstruction as a way to isolate the connected regions of an image.For dilation, reconstruction connects regions marked by local maxima in the seed image: neighboring pixelsless-than-or-equal-to those seeds are connected to the seeded region.
Local maxima with values larger than the seed image will get truncated to the seed value.
Details here
Fix perspective
Fixes perspective using four dots to detect rectangle boundary.
Use the included threshold utility to detect the dots.
Details here
Horizontal line remover
Horizontal line remover.
Developped for Heliasen light barrier.
Removes horizontal noise lines
Details here
Image from distances
Build an image from distance calculation
Details here
Image transformations
Performs various transformations on the image
Details here
K-means clustering
Performs k-means clustering, grouping object with a distance formula
Details here
Median Filter
'Apply median filter
Details here
Normalize Image
'Normalize image
Details here
Otsu merger
Based on Otsu's binarization, create a new image from OTSU channel binarization.
Details here
Partial posterizer
Replaces dominant colors by other colors
Details here
Partial posterizer v2
Replaces dominant colors by other colors. Different algorithm from V1
Details here
Print channels
Print channels
Details here
Pyramid mean shift
Pyramid mean shift: A kind of posterization
Details here
Rotate
Rotates an image according to selected angle
Details here
Simple white balance
Simple white balance: Performs a simple white balance.
https://www.ipol.im/pub/art/2011/llmps-scb/article.pdf
Details here
Temperature and tint
Simple method to alter an image temperature and tint
http://www.tannerhelland.com/5675/simple-algorithms-adjusting-image-temperature-tint/
Details here
Threshold
Creates a mask that keeps only parts of the image
Adaptive threshold
Perform a adaptive threshold.
Morphology operation can be performed afterwards
Details here
Chan Vese
From scikit-image: Chan-Vese segmentation algorithm.
Active contour model by evolving a level set.
Can be used to segment objects without clearly defined boundaries.
Details here
Multi range threshold
Performs range threshold keeping only pixels with values between min and max
for up to 3 channels.
Morphology operation can be performed afterwards.
Masks can be attached, they will be treated as keep masks
Details here
Niblack binarization
Niblack binarization: From skimage - Applies Niblack local threshold to an array.A threshold T is calculated for every pixel in the image using the following formula:T = m(x,y) - k * s(x,y)where m(x,y) and s(x,y) are the mean and standard deviation of pixel (x,y) neighborhood defined by arectangular window with size w times w centered around the pixel. k is a configurable parameter thatweights the effect of standard deviation.
Details here
Otsu
Thresholds image using Otsu binarization
Details here
Otsu overthinked
Based on Otsu's binarization, uses a costum set of channels.
Details here
Range threshold
Performs range threshold keeping only pixels with values between min and max.
Morphology operation can be performed afterwards
Details here
Sauvola binarization
Sauvola binarization: From skimage - Applies Sauvola local threshold to an array.
Sauvola is a modification of Niblack technique.In the original method a threshold T is calculated for every pixel in the image using the following formula:T = m(x,y) * (1 + k * ((s(x,y) / R) - 1))where m(x,y) and s(x,y) are the mean and standard deviation of pixel (x,y)neighborhood defined by a rectangular window with size w times w centered around the pixel.k is a configurable parameter that weights the effect of standard deviation. R is the maximum standard deviationof a greyscale image.
Details here
Splitted range threshold
Performs range threshold with two sets of borders applied inside and outside of linked ROIs.
If no ROIs are provided, all image will be considered within ROI.
Details here
Triangle threshold
Thresholds image using triangle binarization
Details here
Visualization
Visualization tools
IPT Demo
IPT Demo (Image Processing Tool Demo)
A simple showcase of some of the available widgets
Best starting point if you want to build your own widgets
Details here
Calculate chlorophyll
Details here
Edge detectors
Performs edge detection with various common operators.
Mostly used by other tools.
Details here
Print channels
Print channels
Details here
Print color spaces
Print color spaces as individual channels or mosaics.
Details here
Quick shift
From scikit-image: Quick shift segments image using quickshift clustering in Color-(x,y) space.
Details here
ROI manager (deprecated)
Handles ROI edition via user input
Details here
Rotate
Rotates an image according to selected angle
Details here
White balance
Tools to help change white balance, depending on where those tools are set in the pipeline they or may not be ignored when extracting features
CLAHE
Contrast Limited Adaptive Histogram Equalization (CLAHE).
Equalizes image using multiple histograms
Details here
Fix white balance with ROI
Fixes image white balance from ROI that is supposed to be white.
ROI must be present in pipeline.
ROIs must be of type 'keep' or 'delete'.
Only static ROIs are allowed.
Details here
Simple white balance
Simple white balance: Performs a simple white balance.
https://www.ipol.im/pub/art/2011/llmps-scb/article.pdf
Details here