Helminth Egg Automatic DetectorH.E.A.D.

Final User Manual

Copyright c© 2015 I.I. UNAMPUBLISHED BY PUBLISHER

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Licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported License (the“License”). You may not use this file except in compliance with the License. You may obtain acopy of the License at http://creativecommons.org/licenses/by-nc/3.0. Unless requiredby applicable law or agreed to in writing, software distributed under the License is distributed on an“AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions and limitations under the License.First printing, September 2015

Contents

I Part One

1 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.1 System requirements 71.2 Program description/GUI 81.3 Compatible Image Formats/ Image Properties 9

2 Running an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

2.1 Load an Image/set of images 132.2 Image Analysis 142.3 Results 15

II Part Two

3 Contact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

I

1 Getting Started . . . . . . . . . . . . . . . . . . . . . . . 71.1 System requirements1.2 Program description/GUI1.3 Compatible Image Formats/ Image Properties

2 Running an analysis . . . . . . . . . . . . . . . . . 132.1 Load an Image/set of images2.2 Image Analysis2.3 Results

Part One

1. Getting Started

HEAD is an image processing software created on Ruby 2.2.2, which is an interpreted programminglanguage that is executed on JMV (Java Virtual Machine), which makes it a highly portable,multiplatform language.The software’s function is to identify and quantify automatically diverse genera and species ofhelminth eggs that may be contained in microscopy samples of water, soils, excreta and sludge.Its goal is to aid in the analysis and control of this worldwide distributed pathogens of medicalimportance in different facilities around the world.

1.1 System requirements

Since the software is executed on the JMV, a Java Runtime Environment (JRE) or the Java Develop-ment Kit (JDK) must be installed, the latest version of this tools is recommended. This softwarecan be downloaded online in the site: https://java.com/es/download/.Both the JDK and JRE require at least a Pentium 2 266 MHz processor.

Memory Requirements:

• On Windows 64-bit operating systems, in 32- or 64-bit mode, the Java runtime requires aminimum of 128MB of memory.

• For Mac, a processor that executes MacOS X 10.8.3+, 10.9+.

• On Linux, Oracle Linux 6.x (32 or 64 bits) is required or Ubuntu Linux 12.04 LTS, 13.x.

We strongly recommend to use the last version of java, jre or jdk available to avoid errors.To check your version, go to terminal and type:

java -version

8 Chapter 1. Getting Started

To install the last version of java (by the moment) type:

sudo add-apt-repository ppa:webupd8team/java

sudo apt-get update

sudo apt-get install oracle-java8-installer

If you have problems run the program beacuse it is not mark as executable you can type:

sudo chmod +x helmintos-1.4.0-jar-with-dependencies.jar *

*Se cambiará porsteriormente el nombre...

1.2 Program description/GUI

The different functions of each area of the main window are explained in this section.(Main screen image*):Toolbar:

• FileSave all: Saves the numeric results of the analyzed image, or group of images in a .CSV file.Quit: Exits the program

• HelpManual: Opens user manualAbout: Displays developer basic information.

Taskbar:

• Load Image: This function opens the OS system explorer for the user to browse for the imagedesired for analysis. Here you can select one or more images for further analysis.

• Run Analysis: Runs the analysis and helminth egg detection and quantification for a loadedimage, or set of images.

• Occurrences table/Image metrics table, menu: The user can select with information isdisplayed in the data display area (under the image display).

• Sample type selection menu: The software has been programmed to analyze and quantifyhelminth eggs in sample images from different sources, such as reuse water, excreta, soilsand sludge. This menu allows the user to choose the source of the samples for an optimumanalysis. If the user does not select any option, the software will consider reuse water as thedefault source.

Main Screen:

Loaded:In this area of the main screen a list of the files (images) loaded by the user is displayed, if the userselects de “Run analysis” option in the Taskbar this is the list of images that will be analyzed.

Processed:This area displays a list of files that the program has already processed.

Image display area:Displays the last image loaded by the user, once the program starts running the analysis, it displaysthe last image analyzed with every detected object numbered and labeled.

1.3 Compatible Image Formats/ Image Properties 9

Data display area:This area displays the numeric results of the latest analyzed image, in the Taskbar the user canchoose between displaying the occurrence table or the image metrics table:

• Occurrence table: displays the quantification of each helminth egg species (genera) that theprogram detected in each individual image, it also displays the number of objects detectedthat were not considered an helminth egg in a final validation.

• Image metrics table: displays the individual calculated characteristics obtained for eachdetected object in order to perform the classification and labeling of it.

1.3 Compatible Image Formats/ Image Properties

The system works with a pixel by pixel analysis method, and the parameters used for running theanalysis and finding the values for the characteristics is pre-set for images with specific characteris-tics. Important characteristics to consider are image size, resolution, scale and illumination. Thefollowing image characteristics are suggested to obtain optimal results after image processing:

• Camera. A digital camera with a resolution of 1560x1920 pixels is recommended (e.g. uEye).

• Microscope. A Carl Zeiss, model Axiolab A1, with a 10x objective, or any other with similarcharacteristics is recommended.

• Image file format. The recommended file formats are .JPG and .BMP.• Illumination. The following images provide an example of illumination required:

10 Chapter 1. Getting Started

Figure 1.1: Examples Due Due

• Scale. It is one of the most important characteristics needed, the pixel size must be similar to0.4348 um/pixel , if this is not possible, the pixel size needs to be indicated to obtain reliableresults. To help with the pixel size calculation, The next image shows a scale where theminor division is equivalent to 20 micrometers.

1.3 Compatible Image Formats/ Image Properties 11

Figure 1.2: Examples Scale with 20 um annotation in yellow

Next is an example of the size of a helminth egg with respect to the given scale.Also, imageaxes coordinates are indicated as visual aids. Note that the illumination in these images isnot adequate.

Figure 1.3: Fasciola hepatica, (Liver fluke) size comparison against the scale.

2. Running an analysis

The software can perform the analysis of an image or a consecutive analysis of a selected set ofimages. This section explains step by step how to perform the analysis.

2.1 Load an Image/set of images

On the Taskbar click on “Load image” this will open the file browser of your OS, browse and selectany images desired for analysis, once all the images are selected click Open. The list of the loadedimages (including the file location) will be then displayed in a list in the “Loaded” area of the mainscreen.

14 Chapter 2. Running an analysis

Figure 2.1: Load Image

2.2 Image Analysis

Click “Run analysis” to begin the process. The software will perform the analysis of the previouslyloaded image, or the automatic consecutive analysis of all loaded images. Once the process is fin-ished for every image the next message will be displayed at the bottom of the screen: “Recognitiondone. All images have been processed.”

2.3 Results 15

Figure 2.2: Run analysis

2.3 Results

Once the analysis is run on an image, or set of images, the software will display the resultinglabeled image and the numeric result corresponding to that image in the main screen, if a group ofimages was analyzed, the software will display the result of the last image analyzed.

The detection results are generated as follows:

• A labeled image in .PNG format, where all the possible eggs are numbered, highlighted andlabeled with their respective name. As can be seen in the next figure:

16 Chapter 2. Running an analysis

Figure 2.3: Image Result

This file will be generated automatically.• Numeric results, an occurrence table and an image metrics table is also generated and dis-

played in the main screen. The user can select which result is displayed by choosing theoption in the “select table” button in the Taskbar. Unlike the displayed image, the results forall the images are summarized in two tables (one for all the occurrences and one for all theimage metrics). For each of these results a .CSV file can be generated and saved by selectingthe “File - Save all” option in the Toolbar.

These files will be located by default in the same folder containing the analyzed image with thename: labeled(image name).png and session(time of the analysis).csv.

II

3 Contact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Part Two

3. Contact

For further references and information go to:

http://www.iingen.unam.mx/es-mx/Investigacion/Coordinacion/IngenieriaAmbiental/

Paginas/default.aspx