Metadata-Version: 1.1
Name: pygempick
Version: 1.1.9
Summary: Open Source Batch Gold Particle Picking & Procesing for Immunogold Diagnostics
Home-page: https://github.com/jmarsil/pygempick
Author: Joseph Marsilla
Author-email: joseph.marsilla@mail.utoronto.ca
License: MIT
Description-Content-Type: UNKNOWN
Description: 
        pyGemPick: Open Source Gold Particle Picker for Immunogold Diagnostics
        ======================================================================
        
        This is the official installation guide for the PyGemPick module
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        PyGemPick is the cummulation of `Joseph
        Marsilla's <https://github.com/jmarsil>`__ research project under Dr.
        Avi Chakrabartty. This module contains functions that enable filtering,
        detection, and modeling of immunogold particles on TEM micrographs.
        
        The main project goal was to greate an open source batch gold particle
        picking module built in python that could detect gold particles
        regardless of the amount of counterstaining present in the IGEM
        (Immunogold Electron Microscopy) micrograph.
        
        pyGemPick has three main dependencies that are needed before usage
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
            1. [OpenCV (cv2)](https://opencv.org/) 
            2. [Pandas (pd)](https://pandas.pydata.org/)
            3. [Numpy  (np)](http://www.numpy.org/) 
        
        I would suggest installing a new anaconda environment using
        `anaconda <https://conda.io/docs/user-guide/getting-started.html>`__
        terminal into which you can import all the required modules for your
        project. Having trouble installing OpenCv, use the solution outlined
        here: `(install using
        conda) <https://stackoverflow.com/questions/23119413/how-do-i-install-python-opencv-through-conda>`__.
        Pandas and Numpy can also be installed through any terminal using ***pip
        install pandas, numpy***
        
        The project will be updated in the upcoming weeks with tutorials on how
        to use the functions given within
        `pygempick <https://pypi.org/project/pygempick/>`__. This module was
        built to help researchers that are building therasnotic solutions
        (therapy based as well as diagnostic innovations) to help pateints with
        rare protein misfolding diseases like ATTR amyloidosis , `Alzheimer's
        Disease
        (AD) <https://www.alz.org/alzheimers_disease_what_is_alzheimers.asp>`__,
        `Frontotemporal Dementia
        (FTD) <https://www.theaftd.org/what-is-ftd/disease-overview/>`__ and
        `Amyotrophic Lateral Sclerosis (also known as ALS or Lou Gehrig's
        disease) <https://www.als.ca/about-als/what-is-als/>`__ using novel
        Immunogold diagnostic techniques.
        
        ***NEW:*** This update contains supplementary 11 supplementary documents
        that will help you use the module. We cover image compression, image
        picking with singular and duplicate filtering, statistical analysis,
        separation & efficiency tests to test the algorithm's useability.
        
        **Sample Image Data will be provided and shall be located in the DATA
        folder**
        
        Installation
        ------------
        
        ::
        
            pip install pygempick
        
            > import pygempick.core as py
            > import pygempick.modeling as mod
            > import pygempick.spatialstats as spa
        
        Note numpy, pandas and opencv modules dependencies are needed prior installation.
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        **NEW:** This update contains supplementary 11 supplementary documents
        that will help you use the module. We cover image compression, image
        picking with singular and duplicate filtering, statistical analysis,
        separation & efficiency tests to test the algorithm's fairness.
        
        For more information visit the github!
        
        Functions:
        ----------
        
        -  ***py.compress(orig-img)***
        
           -  a function that takes an original large scale electron micrograph
              image and compresses it such that 1px = aproximately one
              nanometer. the exact pixle dimentions for a 3.1x compression are
              given below.
        
        -  ***py.back\_eq(image)***
        
           -  background equalization provided by solution presented
              `here <https://stackoverflow.com/questions/39231534/get-darker-lines-of-an-image-using-opencv>`__
        
        -  ***py.hclap\_filt(p,image, noise)***
        
           -  New High Contrast Laplace Filter.
           -  Applies a `HCLAP
              Kernel <https://en.wikipedia.org/wiki/Discrete_Laplace_operator>`__
           -  Takes odd scaling parameter p > 5 with a regular compressed image
           -  if noise == 'yes' will add median blur after filter applied.
        
        -  ***py.hlog\_filt(p, image, noise)***
        
           -  New High-Contrast Laplace of Gaussian Filter.
           -  Applies a `HCLOG
              Kernel <http://fourier.eng.hmc.edu/e161/lectures/gradient/node8.html>`__
              to each image to produce a single binary image as an output.
           -  Takes odd and even scaling # parameters 18+
           -  input image is regular py.compress image output,
           -  if noise == 'yes' will add median blur after filter applied.
        
        -  ***py.dog\_filt(p, image)***
        
           -  `Difference of Gaussian
              Filter <http://www.tjscientific.com/2017/01/31/using-python-and-opencv-to-create-a-difference-of-gaussian-filter/>`__.
              Input is an odd number p to determine size of DOG kernel,
           -  input is an py.compress output image,
           -  if noise == 'yes' will add median blur after filter applied.
        
        -  ***py.bin\_filt(p, image)***
        
           -  Smart Binary Filtering. Uses the average gray pixel intensity
              values to determing the starting `threshold
              position <https://docs.opencv.org/2.4/doc/tutorials/imgproc/threshold/threshold.html>`__.
           -  Takes odd scaling parameter p, input image is a py.compress output
              image
        
           ***Note:*** TEM migrograph filtering using simple binary thresholding
           was first completed in 2003 with one of the first gold particle
           picking algorithms
           `GoldFinder <https://www.sciencedirect.com/science/article/pii/S104784770200624X>`__.
        
        -  ***New: key\_filt(keypoints1, keypoints2)***
        
        -  Allows you to scandetected keypoints and eliminate duplicates! Allows
           you to detect partciles with more than one filter. Returns updated
           keypoints 1 with the removed keypoints and number of duplicate(s)
           detected.
        
        -  ***py.pick(image, minAREA, minCIRC, minCONV, minINER, minTHRESH)***
        
           -  Input image is a binary image from one of the above filters, next
              have to set the parameters to optimize `OpenCv's Simple Blob
              Detector <https://www.learnopencv.com/blob-detection-using-opencv-python-c/>`__
           -  Detects immunogold particles on filtered binary image by
              optimizing picking across 4 main paramaters using OpenCv's simple
              blob detector.
           -  Have to optimize picking for each set separately on a per class or
              per trial basis.
        
           .. rubric:: Gold Particle Picking Parameters
              :name: gold-particle-picking-parameters
        
           ::
        
               1. minArea = lowest area in pixels of a detected gold particle (20 px**2)
               2. minCirc = lowest circularity value of a detected gold particle [.78 is square]
               3. minConv = lowest convextivity parameter which is  Convexity is defined as the (Area of the gold particle / Area of it’s convex hull)
               4. minINER = minimum inertial ratio (filters gold particles based on  eliptical properties, 1 is a complete circle)
        
        -  ***py.snapshots(folder, keypoints, gray\_img, i)***
        
           -  folder = folder location where snapshots will be saved, keypoints
              = the detected keypoints from py.pick function , gray\_img =
              compressed grayscale image, i = image number.
        
           -  Takes an compressed grayscale image and uses the detected
              keypoints as a marker to take a snapshot of within a 100px radius
              of that gold particle's position. *Researchers use this to analyze
              the morphological properties of protein aggregates*
        
        -  ***mod.draw(n, test\_number, noise, images)***
        
        function to draws test micrograph sets that will be used in subsequent
        efficiency or separation tests.
        
        ::
        
            1. Test number 1 is draw only circles, 2 is draw both circles and ellipses. 
            2. Noise if == 'yes' then, randomly distibuted gaussian noise will be drawn 
                according to mu1, sig1. 
            3. images are the number of images in the set - used with n which is number of 
               particles detected in the actual set to calulate the particle density of model 
               set.
               
        
        -  ***mod.imgclass(inv\_img)***
        
           -  Uses a compressed grayscale image from
              `cv2.cvt\_color(RGB2GRAY) <https://docs.opencv.org/2.4/modules/imgproc/doc/miscellaneous_transformations.html>`__
              and returns the intensity histogram and related bins position w/
              im\_class.
        
        -  ***mod.septest(p,image)***
        
           -  Let p be a range of integers ranging from [1, x], let image be a
              grayscale image produced after original image compression and
              conversion to grayscale using OpenCv's function
              cv2.cvtColor(orig\_img, cv2.COLOR\_RGB2GRAY).
        
           -  Completes separation test for single filter comparrison.
        
        -  ***New mod.septest2(p, image, hlogkey)***
        
           -  let p be a range of integers ranging from [1, x] , let image be a
              grayscale image produced after original image compression and
              conversion to grayscale using OpenCv's function
              cv2.cvtColor(orig\_img, cv2.COLOR\_RGB2GRAY).
        
           -  hlogkey = the keypoints of detected image fitered with HLOG filter
              - this ensures faster particle detection since we aren't running
              the same filtering step more than once!
        
           -  Completes separation test for ***dual high-contrase filter
              comparrison***.
        
        -  ***mod.fitpcf(data)***
        
           -  Data is the input from a csv created by sta.bin2csv
           -  file is in format of pcf-dr#-error.csv'.
           -  Function initially created to plot graphs for image set with
              varrying concentrations of AB aggregates in solution
        
           | **Output:** built to produce one graph, with fitted curve for
             positive control(s).
           | Equation fitted to probability distribution for Complete Spatial
             Randomness of the distribution of IGEM particles across EM
             micrographs.
        
        -  ***spa.gamma(a,b,r)***
        
           -  a = width of image in pixels
           -  b = height of the image in pixels
           -  r is the diatance of the donut from which correlation was
              calculated.
        
           Function taken from work by `Philemonenko et al
           2000 <http://nucleus.img.cas.cz/pdf_publications/PHI_Statistical%20evaluation%20of%20Colocalization%20Patterns_01.pdf>`__
           that was used as a window covariogram to correct `Ripley's K
           function <http://wiki.landscapetoolbox.org/doku.php/spatial_analysis_methods:ripley_s_k_and_pair_correlation_function>`__
           for boundary conditions.
        
        -  ***spa.pcf(r, N, p0, p1)***
        
           -  r is the radius of the donut taken with bin width dr.
           -  N is the degree PCF (Pair Correlation Function) is the probability
              distribution of a CSR related process that we will used to fit our
              normalized version of
        
           -  This is a python based solution to `Philmoneko's Statistical
              Evaluation of Colocalization Patterns in Immunogold Labeling
              Experiments <http://nucleus.img.cas.cz/pdf_publications/PHI_Statistical%20evaluation%20of%20Colocalization%20Patterns_01.pdf>`__.
              The PCF distribution for calculating the colocolization of
              immunogold particles on transmission electorn microgrpahs is
              represented here.
        
        -  ***spa.record\_kp(i, keypoints, data)***
        
           -  i is the image number counter
           -  keypoints is the list of keypoints of Gold particles detected by
              py.pick
           -  data is an empty pandas dataframe.
        
           This function recods the x,y positions of the keypoints detected in
           each image. Run in for loop to add results for each image to
           dataframe which can be then exported into a csv for easy access.
           (completed in spa.bin2csv )
        
        -  ***spa.bin2csv(images)***
        
        -  function takes a list of filelocations from glob.glob (asks for the
           filtering parameters) then it outputs a csv of the x and y
           coordinates of keypoints for every image in images. (For example, row
           1 contains the x coordinate of the keypoints in image 1 and row 2
           contains the y coordinates in image 1 ect...)
        
        -  ***spa.bin2df(images)***
        
           -  images is a set of images from folder using glob.glob() function,
        
           -  Output records the keypoint positions found in each image and
              outputs a pandas df with detected keypoint centers in (x,y) pixel
              coordinates.
        
        -  ***spa.csv2pcf(data, dr)***
        
           -  takes the filename ``data`` from a csv produced by bin2csv() and
              outputs non-normalized scale invarient k (cross-corelation) and
              pcf (pair-correlation) statisticaldata from the spatial
              distribution of the paticles on each micrograph. (determines
              wheter the nul-hypothesis of CSR `Complete Spatial
              Randomness <https://en.wikipedia.org/wiki/Complete_spatial_randomness>`__
              is upheld or voided...). Analyzed by bin2csv. Example output
              provided in docs.
        
           -  dr is the donut width as defined by philmonenko et al, 2000
        
        -  ***spa.keypoints2pcf(data\_set, dr)***
        
           -  Input folder with CSV files of keypoints for different tests Need
              to know Image number and average particles detected in each set
              (**example**: data\_set =
              glob.glob('/home/joseph/Documents/PHY479/Data/anto/\*.csv'))
        
           -  dr is the donut width as defined by `philmonenko et al, 2000
              article <http://nucleus.img.cas.cz/pdf_publications/PHI_Statistical%20evaluation%20of%20Colocalization%20Patterns_01.pdf>`__
              on immunogold particle colocolization and spatial statistcs.
        
           -  **output:** pcf-dr{}-error.csv - columns dr (sampling radius), pcf
              (`pair correlation
              coefficient <https://en.wikipedia.org/wiki/Pearson_correlation_coefficient>`__),
              dpcf (propogated uncertainty in pcf)
        
Keywords: immunogold batch gold particle picker EM micrograph processing correlation       analysis IGEM diagnostics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: Unix
Classifier: Topic :: Education
Classifier: Topic :: Utilities
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Mathematics
