Image_Analysis_App.ImageSeg_App

class Image_Analysis_App.ImageSeg_App(master)

Bases: object

A class used to create the Image Segmentation App

masterTK()

TK toplevel object to initialize the application

credits()

Prints the credits for this application on the status screen

help_info()

Prints help information for this application based on the user’s choice

read_files()

Allows the user to select the images needed for analysis

bttn(window, text, bcolor, fcolor, command)

window : top level object text : str bcolor : str fcolor : str command : method Creates the buttons for the custom analysis window

default_analysis()

Performs the default analysis operations for the images provided.

custom_analysis()

Allows the user to customize the analysis for their images

analyze()

Creates the window for the user to choose their analysis option.

recent_image()

Allows the user to access the most recently created image.

previous_image()

Allows the user to access the image created prior to the most recent one

original_image()

Allows the user to access the original image essentially resetting their analysis.

recent_mask()

Allows the user to access the most recently created mask

previous_mask()

Allows the user to access the mask created prior to the most recent mask

skeleton_dilate()

Allows the user to dilate the skeleton mask loaded in to isolate their region of interest

median_image()

Allows the user to perform a median filter operation through the customization window

background_subtract()

Allows the user to perform a background subtract operation through the customization window

sobel_image()

Allows the user to perform a sobel filter operation through the customization window

ahe()

Allows the user to perform an adaptive histogram equalization operation through the customization window

rescale_intensity()

Allows the user to perform a rescaled intensity operation through the customization window

multiotsu()

Allows the user to perform a multiotsue mask operation through the customization window

otsu()

Allows the user to perform an otsu mask operation through the customization window

yen()

Allows the user to perform a yen mask operation through the customization window

li()

Allows the user to perform a li mask operation through the customization window

defaul_morph()

Allows the user to use the default morphology operations used in the default analysis

closing_morph()

Allows the user to use the closing morphology operation through the customization window

opening_morph()

Allows the user to use the opening morphology operation through the customization window

dilation_morph()

Allows the user to use the dilation morphology operation through the customization window

erosion_morph()

Allows the user to use the erosion morphology operation through the customization window

properties_table()

Creates the table with properties from the analysis as selected by the user

props()

Allows the user to select what properties they would like to include in their analysis

export()

Exports the properties table as an excel file

__init__(master)

Methods

__init__(master)

ahe()

Performs the adaptive histogram equalization operation from scikit image.

analyze()

Intialize the window for the user to choose their analysis option: Default or Custom

background_subtract()

Function for the background subtraction button.

bttn(window, text, bcolor, fcolor, command)

Creates the buttons for the custom analysis.

closing_morph()

Perfroms the closing morphology operation.

credits()

Returns the credits for this program.

custom_analysis()

Function for the user to customize their analysis process.

default_analysis()

Default analysis operation for loaded image.

default_morph()

Performs the default morphology operation.

dilation_morph()

Performs the dilation morphology operation.

erosion_morph()

Performs the erosion morphology operation.

export()

Exports an excel sheet of the region propery information obtained.

help_info()

Provides some help information about how to use the program.

label_image()

This will create labels for the image.

li()

Li mask morphology operation.

median_image()

Function for the median filter button.

multiotsu()

MultiOtsu mask morphology operation.

opening_morph()

Performs the opening morphology operation.

original_image()

Accesses the original image, esentially resetting the analysis

otsu()

Otsu mask morphology operation.

previous_image()

Accesses the image created prior to the most recent one

previous_mask()

Accesses the mask created prior to the most recent one

properties_table()

Creates the table of properties for analysis.

props()

Obtains properties of the identified regions of interest.

read_files()

Loads the images in to perform analysis on.

recent_image()

Accesses the most recent image created.

recent_mask()

Accesses the most recent mask created.

rescale_intensity()

Performs the rescale intensity operation from scikit image.

skeleton_dilate()

Function to dilate the skeleton loaded in by the user to isolate to their region of interest.

sobel_image()

Performs the sobel operation from scikit image.

yen()

Yen mask morphology operation.

ahe()

Performs the adaptive histogram equalization operation from scikit image.

In addition, this function will multiply the adaptive histogram equalization image will be multiplied to the previous image passed in to enhance the contrast.

analyze()

Intialize the window for the user to choose their analysis option: Default or Custom

background_subtract()

Function for the background subtraction button. Subtracts the background from the image.

Asks the user for the gaussian sigma value to use. The default value is 7. If the user does not provide a value, will simply cancel the operation.

bttn(window, text, bcolor, fcolor, command)

Creates the buttons for the custom analysis.

closing_morph()

Perfroms the closing morphology operation.

credits()

Returns the credits for this program.

custom_analysis()

Function for the user to customize their analysis process.

This contains all of the possible analysis options available to the user. This initializes a different napari viewer from the default analysis, and will stop the default analysis viewer from continued use if one was created prior to this.

default_analysis()

Default analysis operation for loaded image.

Will initialize the image analysis function with the default parameters without any customization. Creates a napari viewer used only for the default analysis.

default_morph()

Performs the default morphology operation.

This operation consists of dilation and closing morphology steps.

dilation_morph()

Performs the dilation morphology operation.

erosion_morph()

Performs the erosion morphology operation.

export()

Exports an excel sheet of the region propery information obtained. This exports the table created from the proerties_table function

help_info()

Provides some help information about how to use the program.

label_image()

This will create labels for the image.

The returned labels are regions of interests determined by the final mask after all of the analysis is done. Getting these labels will set analysis to complete and allow for properties to be exported

li()

Li mask morphology operation.

Uses the current image and doesn’t require any args.

median_image()

Function for the median filter button. Performs the median filter operation from scikit image.

Asks the user for the cube width value to use. The default value is 3. If the user does not provide a value, will simply cancel the operation.

multiotsu()

MultiOtsu mask morphology operation.

Uses the current image and doesn’t require any args.

opening_morph()

Performs the opening morphology operation.

original_image()

Accesses the original image, esentially resetting the analysis

otsu()

Otsu mask morphology operation.

Uses the current image and doesn’t require any args.

previous_image()

Accesses the image created prior to the most recent one

previous_mask()

Accesses the mask created prior to the most recent one

properties_table()

Creates the table of properties for analysis.

This is created from the labels generated and based on the properties you selected.

props()

Obtains properties of the identified regions of interest.

This is based on the labels obtained. This step cannot be performed if the analysis is set to complete. Properties can be changed based on what the user selects when prompted

read_files()

Loads the images in to perform analysis on.

recent_image()

Accesses the most recent image created.

recent_mask()

Accesses the most recent mask created.

rescale_intensity()

Performs the rescale intensity operation from scikit image.

Asks the user for the minimum and maximum intensity value to use. The default values are 0 (minimum) and 255 (maximum). If the user does not provide a value, will simply cancel the operation.

skeleton_dilate()

Function to dilate the skeleton loaded in by the user to isolate to their region of interest.

sobel_image()

Performs the sobel operation from scikit image.

yen()

Yen mask morphology operation.

Uses the current image and doesn’t require any args.