fibermorph 0.1.4

Toolkit for analyzing hair fiber morphology

fibermorph

Python package for image analysis of hair curvature and cross-section

Prerequisites

We recommend that you use a virtual environment to run fibermorph in a virtual environment to avoid any conflicts with other Python packages you might have on your system. To learn more about virtual enviornments, click here.

If you are familiar with Python, conda and have the necessary installations on your system, feel free to skip ahead to the section entitled "Install the package", otherwise you can follow the step by step instructions below for the prerequisites.

Setting up

1. We recommend you download miniconda for your operating system.

You may also download Anaconda. The only difference is that Anaconda comes preloaded with more libraries (500 Mb). You won't need this to run fibermorph, so we recommend you stick to minconda which is the smaller (58 Mb) and quicker to download.

Whichever you choose be sure to download the version with Python 3.X and not Python 2.X.

2. Open a terminal.

The commands are written in bash, so if you are running this on a Windows OS, you will need to switch into the correct settings. You can find more information for Windows specifically here.

3. Now you can set up a virtual environment.

Create an empty conda environment, e.g. conda create -n <YearMonthDay>_fibermorph python=3.8 and load it conda activate <YearMonthDay>_fibermorph

You are now ready to install fibermorph!

Install the package

1. After having activated your new virtual environment, you can simply run pip install fibermorph.

You can find the latest release here on this GitHub page and on the fibermorph PyPI page.

2. You have successfully installed fibermorph.

The package is now ready for use. Enter fibermorph -h or fibermorph --help to see all the flags. You can keep reading to try out the demos and read instructions on the various modules within the package.

Demo data

Before using this on any of your own data, it's recommended that you test that you test whether fibermorph is working properly on your machine. There are a few demo modules you can use to check whether fibermorph is running correctly.

Testing with real data

You can test both the curvature and section modules with real data that is downloaded automatically when you run the --demo_real modules.

In both cases, all you need to do is specify a folder path where the images and results can be created with ---output_directory or -o. This folder can be existing, but you can also establish a new folder by including it in the new path.

Both modules will download the demo data into a new folder tmpdata within the path you gave. Then, fibermorph will run the curvature or section analysis, and the results will be saved in a new folder results_cache at this same location. It is recommended that you specify a path with a new folder name to keep everything organized.

Testing curvature analysis

--demo_real_curv

This flag will run a demo of fibermorph curvature analysis with real data. You will need to provide a folder for the demo data to be downloaded.

To run the demo, you will input something like: fibermorph --demo_real_curv --output_directory /Users/<UserName>/<ExistingPath>/<NewFolderName

Testing section analysis

--demo_real_section

This flag will run a demo of fibermorph section analysis with real data. You will need to provide a folder for the demo data to be downloaded.

To run the demo, you will input something like: fibermorph --demo_real_section --output_directory /Users/<UserName>/<ExistingPath>/<NewFolderName

Calculating image analysis error

In order to validate the image analysis program, the fibermorph package includes two modules that will generate and analyze dummy data, then run the appropriate analysis and generate error data.

Both --demo_dummy modules require the following flags:

-o , --output_directory
                        Required. Full path to and name of desired output directory.
                        Will be created if it doesn't exist.

--repeats               Integer. Number of times to repeat validation module
                        (i.e. number of sets of dummy data to generate).

The modules create a results_cache within the given path. In this folder there will be another folder named <MonthDay_HourMinute>_ValidationTest_<Curv or Section> where the generated dummy images and corresponding parameters in spreadsheets will be in a folder named ValidationData and the error data will be in a folder named ValidationAnalysis.

Running the module once will create a set of data and analyses for a single randomly generated arc and line (for curvature) or circle and ellipse (for section). To produce more data, simply add the flag --repeats with the number of times you would like to repeat it, e.g. fibermorph --repeats <integer>. This flag is optional.

Validating curvature analysis

--demo_dummy_curv

This flag will run a demo of fibermorph curvature with dummy data. Arcs and lines are generated, analyzed and error is calculated.

For this module, you can optionally include --window_size. This will allow you to edit the window size used to fit the circle used to estimate curvature. By default, this is 10 pixels. The images generated are 3900 x 5200 pixels, and you can use a range of values between 10 and 3900.

To run the demo, you can enter e.g. fibermorph --demo_dummy_curv --output_directory /Users/<UserName>/<ExistingPath>/<NewFolderName> --repeats 4

Rather than repeating this analysis with various window_sizes, you can simply use the curvature module (see below) and set the --input_directory to the /ValidationData folder created above. You will need to set --resolution 1, --window_size 10, and --window_unit px or whatever number of pixels you would like to use as a window size.

Validating section analysis

--demo_dummy_section

This flag will run a demo of fibermorph curvature with dummy data. Arcs and lines are generated, analyzed and error is calculated.

To run the demo, you can enter e.g. fibermorph --demo_dummy_section --output_directory /Users/<UserName>/<ExistingPath>/<NewFolderName> --repeats 4

Deleting demo folders

--delete_dir Can be used to delete directories generated in the demo modules.

Example usage: fibermorph --delete_dir --output_directory /Users/<UserName>/<ExistingPath>/<ResultsFolderName>

This will delete the folder (with all its contents) and print a confirmation of which folder has been deleted.

Using the fibermorph packages

The main modules of the fibermorph package are --curvature and --section. Both require the following flags to run:

-o , --output_directory
                        Required. Full path to and name of desired output directory. Will be created
                           if it doesn't exist.
-i , --input_directory
                        Required. Full path to and name of desired directory containing input files.
--jobs                  Integer. Number of parallel jobs to run. Default is 1.

Curvature

To calculate curvature from grayscale TIFF images of hair fibers, the flag --curvature is used with the following flags in addition to input and output directories:

--resolution_mm       Integer. Number of pixels per mm for curvature analysis.
--window_size  [ ...]
                      Float or integer. Desired size for window of measurement for curvature
                      analysis in pixels or mm (given the flag --window_unit). Default is 10.
                      Works when the --window_unit is pixels.
--window_unit {px,mm}
                      String. Unit of measurement for window of measurement for curvature
                      analysis. Can be 'px' (pixels) or 'mm'. Default is 'px'.
-s, --save_image      Default is False. Will save intermediate curvature processing images if
                      --save_image flag is included.
-W, --within_element  Boolean. Default is False. Will create an additional directory with
                      spreadsheets of raw curvature measurements for each hair if the
                      --within_element flag is included.

So, to run a curvature analysis, you would enter e.g.

fibermorph --curvature --input_directory /Users/<UserName>/<ImageFolderPath> --output_directory /Users/<UserName>/<ExistingPath>/ --window_size 0.5 --window_unit mm --resolution 132 --save_image --within_element --jobs 2

Section

To calculate cross-sectional properties from grayscale TIFF images of hair fibers, the flag --section is used with the following flags:

--resolution_mu       Float. Number of pixels per micron for section analysis.
--minsize             Integer. Minimum diameter in microns for sections. Default is 20.
--maxsize             Integer. Maximum diameter in microns for sections. Default is 150.

An example command would be:

fibermorph --section --input_directory /Users/<UserName>/<ImageFolderPath> --output_directory /Users/<UserName>/<ExistingPath>/ --minsize 30 --maxsize 180 --resolution_mu 4.25 --jobs 2

Converting raw images to grayscale TIFF

This package features an additional auxiliary module to convert raw images to grayscale TIFF files if necessary: --raw2gray

In addition to the input and output directories, the module needs the user to specify what file extension it should be looking for.

--file_extension      Optional. String. Extension of input files to use in input_directory when
                      using raw2gray function. Default is .RW2.

A user could enter, for example:

fibermorph --raw2gray --input_directory /Users/<UserName>/<ImageFolderPath> --output_directory /Users/<UserName>/<ExistingPath>/<NewFolderName> --file_extension .RW2 --jobs 4