Comparative Study of DICOM Files

Handling Software’s: Study Based

on the Anatomage Table

Zineb Farahat1(&), Mouad Hasni1, Kawtar Megdiche2,

Nissrine Souissi3, and Nabil Ngote1
1
Abulcasis International University of Health Sciences, Rabat, Morocco
[email protected]
2
Medical Simulation Center of the Cheikh Zaid Foundation, Rabat, Morocco
3
Department of Computer Science, MINES-RABAT School, Rabat, Morocco

Abstract. The DICOM format is complex due to the number of information

that these files must contain. Therefore, different software were developed in
order to ensure the proper handling of DICOM files. In this paper, we first
understood the structure of a DICOM file by using a proprietary raster graphics
editor named Photoshop. Then we studied the existing software, which can
handle the DICOM files. This study is based on the Anatomage table of virtual
dissection used in the Cheikh Zaid Foundation Medical Center that we also tried
to extend by the missing features. To add annotations to this table; we first used
a VBA (Visual Basic for Applications) code and then we added these annota-
tions directly to a copy of the CSV (Comma-separated values) file of the
annotations, which is taken from the Anatomage table. The doctors can prepare
their courses as well as some quizzes for their students by adding their own
annotations to the 3D pathologic reconstructions done in the Anatomage table.

Keywords: DICOM
Annotation
Benchmarking
Virtual dissection table

Anatomage table
VBA

1 Introduction

Nowadays, and specifically with large amounts of medical images acquired by modern
modalities [1, 2], medical imaging has evolved to digital. In this context, the exchange
of data between different equipment from different suppliers has become more and
more numerous. For the implement of communication between the medical image
equipment, the standard of Digital Imaging and Communications in Medicine
(DICOM) is constituted, which embodies several major enhancements to previous
versions of the ACR-NEMA Standard [3]. The DICOM does not present a simple
image format, it is rather expanded, and it presents communication techniques and
exchange between the different modalities used in medical imaging [4].
Moreover, the large amount of information stored in a DICOM file mainly explains
the use of a complex platform to manage them [5]. Indeed, Anatomage has developed a
virtual dissection table of the human body in real size [6] that can read and handle
DICOM files. In addition to that, several hundred cases are implemented by the
© Springer Nature Switzerland AG 2020
M. Serrhini et al. (Eds.): EMENA-ISTL 2019, LAIS 7, pp. 390–399, 2020.
https://doi.org/10.1007/978-3-030-36778-7_43
 Comparative Study of DICOM Files Handling Software’s 391

manufacturer in the Anatomage Table. Virtual dissections on the Anatomage

Table make its utilization simple because it did not need chemical treatment and it is
fully reusable [7–9].
This study is based on the Anatomage table of virtual dissection [10] used in the
Cheikh Zaid Foundation Medical Center that we tried to extend by the missing features
by adding annotations to this table. In this paper, we propose a new approach based on
the use of Anatomage Table as a diagnostic tool [7] and an innovative learning tool in
medicine [9] to define different criteria. To conduct this study, two questions we tried to
answer: how is a DICOM file organized? Moreover, how to manage this kind of files?
In fact, we first tried to understand the structure of a DICOM file, then to create a
new one using proprietary software. After that, a comparative study was carried out to
retain two image processing software’s that are used in the handling of DICOM files,
and that meet the most predefined criteria using a Benchmarking.
Otherwise, we took the application TableEDU 4.0 of the Anatomage Table [7, 10]
as a main example of a perfect tool of handling DICOM files, knowing that it is used in
the Cheikh Zaid Foundation Medical Center for medical training not only in its ped-
agogical side [10], but also as a diagnostic tool [7].
The approach of the research is made using the same dataset, by opening com-
puterized tomography (CT) images and magnetic resonance imaging (MRI) in different
software. The rest of paper is organized as follows. Section 2 depicts an overview of
DICOM. Section 3 is devoted to the materials and methods. Section 4 depicts results
and discussion. Finally, conclusions are mentioned in Sect. 5.

2 An Overview of DICOM

The DICOM is a standard that was created by the American College of Radiology
(ACR) in association with the NEMA. It is standard norm for the informatics manage-
ment of data issued from the medical imagery. The purpose of this norm is to improve the
communication of the data regardless of device manufacturer, facilitate the development
and expansion of the archiving system and the image communication as well [4].
The DICOM format differs from other image formats once it deals with its information.
A DICOM file consists of a header and image data sets, all packed into a single file
[Figure]. The first few packets of information in it constitute the “header.” It stores
demographic information about the acquisition parameters, patient, for the imaging
study, matrix size, image dimensions, color space, and a host of additional non-intensity
information required by the computer to correctly display the image [11]. Each header
begins with a preamble of 128 bytes usually set to zero followed by 4 bytes to write the
characters ‘D’. ‘I’. ‘C’. ‘M’. As a result of the preamble, all kinds of information follow
one another. They are organized into several groups of information. Each data element
consists of three data fields if VR is implicit and four fields if VR is explicit. All of this
data represents a DICOM data dictionary [11]. The header data information is encoded
within the DICOM file so that it cannot be accidentally separated from the image data. If
the header is separated from the image Data, the computer will not know which imaging
study had been done or to whom it belongs and it will not be able to display the image
correctly, leading to a potential medicolegal situation [11] (Fig. 1).
392 Z. Farahat et al.

Fig. 1. Structure of a DICOM image file [11].

The DICOM standard is an object-oriented language. Each DICOM object, usually

an image, contains both information (patient’s name, image pixels, etc.) and functions
(print, save, etc.) that this information must undergo. The DICOM processing of
information therefore consists in matching an object DICOM (Information Object) to a
specific function (Service Class). This combination is called (Service/Object Pair) or
(SOP) (Fig. 2) [11].

Fig. 2. Combination (Service/Object Pair) of a DICOM file [13].

The software Adobe Photoshop permits to associate to the forms drawn and saved
as DICOM format a list of attributes. These shown attributes contain the Data Tag
Element, which is an ordered pair of 16-bit integers representing the group number, and
followed by the element number. It indicates the type of information that will follow. It
is broken down into 2 sets of 2 bytes, the first 2 bytes encode a group of information
and the next 2 bytes specify the element of the group (Fig. 3).
 Comparative Study of DICOM Files Handling Software’s 393

Fig. 3. Attributes of DICOM file

There is a complete list of possible values for the “Tag” field. The table below
shows the most frequently used main groups of information (Table 1):

Table 1. Group of Information [13].

Group of Signification
information
0008 Meta information (Meta Information File, SOP Class UID…),
Identification of the center (Examination date, Type of examination,
Manufacturer of the machine, Hospital, Identification of the machine…)
0010 Information about the patient (Name, Date of birth, Sex…)
0018 Information on the acquisition of information (cutting thickness, kV
parameters, time, patient position, etc.)
0020 Positioning and information relating to the acquisition (patient orientation,
series, reference plane, number of images in the acquisition…)
0028 Presentation of the image (dimensions, grayscale, color tables, allocated
bits, stored bits, most meaningful bit…)
4000 Text
7FE0 pixel data

In addition to that, the software Adobe Photoshop uses DCMTK (DICOM Toolkit);
which is a set of libraries written in C++ permitting to examine, create and convert
DICOM files.

3 Materials and Methods

3.1 Materials

Anatomage Table. The Anatomage Table is a table of virtual dissection [9, 12]
realized to help the students to better understand their course of anatomy. It is run by
windows 7 and uses the application TableEDU 4.0, which is pre-installed in the table
by the constructor. This table permits to read and open the DICOM Files issued from
394 Z. Farahat et al.

different modalities of medical imagery. The Anatomage Table permits the 3D

reconstruction from several complementary 2D images.
Adobe Photoshop. The software Adobe Photoshop, which is a software of treatment,
retouch and drawing, used in all systems of exploitation such as windows and
MacOS… permits the image saving under several formats such as DCM, JPEG,
PNG…
TableEDU 4.0. In the medical field, several software is used to read and manipulate
the DICOM Files. To keep the most reliable, a study of the existing is initialized. Based
on the TableEDU 4.0 application, some choices criteria are defined, whose we can cite
the fact that software must be Opensource to be able to modify it when necessary, the
availability of documentation, the display of the attributes, the export and import of the
DICM Files, the image modification, the 3D reconstruction.
VBA Language. The VBA is a programming language that allows the use of Visual
Basic code to run many features of the Excel application. A program written in VBA is
often called a macro.

3.2 Methods

Comparative Study. To carry out this comparative study and Benchmark we fol-
lowed the steps bellow.
– Identify the Search Engines (Google Scholar, SpringerLink DL…).
– Define Keywords. The key words we used are: Application/Software, DICOM files,
create, edit, remove, open source, compare, and manage.
– Define the Number of Applications to Compare. We have set the number to eight
software.
– Define the Comparison Criteria. Documentation, open source software, free soft-
ware, operating system adapted to the one used at the medical simulation center of
the Cheikh Zaid Foundation, programming language, export, import, registration in
DICOM format, storage in the application, display information specific to DICOM
files, reading DICOM files in 2D, 3D reconstruction from 2D images, simultaneous
display of several sections.
– Define the Rating System. We assigned a score (from 0 to 5) to each criterion with:
0–1: Unacceptable, 2: Weak, 3: Good, 4: Very Good, 5: Excellent.

Adding of Annotations. To add annotations to the 3D reconstructions done by the

embarked application TableEDU 4.0 of the Anatomage table, two tendencies were
followed to modify the original file of annotations. The first one is the automatic adding
of annotations lines by a VBA code (Fig. 4) by creating some command buttons as well
as many boxes to fill in by the name of the wanted organ, besides its system.
 Comparative Study of DICOM Files Handling Software’s 395

Fig. 4. The VBA code.

Fig. 5. The window generated by the code.

396 Z. Farahat et al.

By clicking on the command button “Add” (Fig. 5), a new line is added to the chart
of annotations. However, the added annotation does not appear on the list of annota-
tions of the Anatomage Table, which is explained by the difference between the format
known by the Anatomage table (CSV) and the format of the file modified by the VBA
Language (Excel). This led to a second tendency, which consists of recuperating a copy
of the original file containing the annotations, which is in a CSV format, from the
Anatomage Table and modifying it directly in our computers. For this reason, we had
to open this file with Open office to keep the same CSV format by choosing as a
character set Unicode “UTF-8” and as a means of separation “Tabulation”, then to add
manually some lines of annotations to the chart. The last step consists of saving the
modifications and transferring the new file to the Anatomage Table. The TableEDU 4.0
application permits to save the new spatial coordination’s of annotations (Fig. 6).

Fig. 6. Added three lines on the CSV file.

4 Results and Discussion

4.1 Results of Comparison Study

This study was realized using magnetic resonance imaging (MRI) images taken in the
Cheikh Zaid hospital of Rabat of a breast of a patient and computerized tomography
(CT) scans of a road polytrauma patient of the same health foundation. The study of the
existing has been summarized as a cartography form containing 8 software to which
some points on a scale of 0 (The software doesn’t respond to the defined criteria) to 5
(The software responds perfectly to the defined criteria) were attributed. This analysis
was based on different criteria taken from the use of the Anatomage Table that provides
a simple and interesting handling of DICOM file [7]. This permitted to create a Radar
chart (Fig. 7) and to choose two software responding the most to the criteria.
 Comparative Study of DICOM Files Handling Software’s 397

Fig. 7. Radar chart summarizing the Benchmark.

On this Radar chart (Fig. 7), both Weasis and 3D Slicer software occupy the
majority of the surface of the circle, the reason why we can say that they are the
software responding the most to the criteria.
3D Slicer. The 3D slicer is a software of reading and manipulation of medical images.
It permits to display the information linked to DICOM files in addition to modifying
the image parameters. This software had advantages such as; to do 3D reconstructions
from 2D images issued from different modalities of medical energy, besides comparing
simultaneously several views and to measure distances. The source code of this soft-
ware is accessible so there will be a possibility to complete it by many missing
functionalities if needed. A thing that was done by some searchers who added different
extensions and modules (130 modules and more than 74 extensions).
Weasis. Weasis is a software of visualization that permits to update the images
DICOM, a simultaneous reading is comparison of many images by modifying the
cutting plan. Moreover, this software permits to add some annotations, do some
measures adjust the brightness and contrast scale of the image, add signs and forms
geometric to design the wanted parts and to display the attributes and the information
linked to the DICOM files.
Comparison of the Two Software. Each of the two software has both advantages and
limits as well. On one hand, Weasis permits to do measures and add annotations.
However, this software does not permit to do 3D reconstructions. One the other hand,
the 3D software slicer permits to do 3D reconstructions as well as measurement but
without adding annotations.
398 Z. Farahat et al.

4.2 Adding of Annotations to 3D Reconstructions Done

by the Anatomage
Thanks to the method explained previously, Annotations and explanations can there-
fore be added to 3D reconstructions done in the Anatomage table.

Fig. 8. Added annotations on the application TableEDU 4.0.

In the figure above (Fig. 8), the annotations added to the Anatomage table in CSV
format have been attributed to the 3D reconstruction made using the images taken by a
computerized tomography (CT) of the road polytrauma patient.

Fig. 9. Saving Added annotations on the 3D reconstruction.

As shown in the figure above of the 3D reconstruction done using images taken by
a magnetic resonance imaging (MRI) (Fig. 9), by clicking on the annotations dis-
placement tool in the Volume Visibility dialog box we choose their ideal location. The
Anatomage table allows saving spatial coordination’s annotations automatically thanks
to the TableEDU 4.0 application’s tools. Furthermore, the doctors of Cheikh Zaid
foundation can prepare their courses as well as some quizzes for their students by
adding their own annotations and explanations to 3D pathologic reconstructions real-
ized by images taken by different modalities.
 Comparative Study of DICOM Files Handling Software’s 399

5 Conclusion

This study led us to understand the structure of a DICOM file by using a proprietary
software called Photoshop, then to manage and manipulate DICOM files using a
software too. A study of the existing DICOM Files Handling Software’s has been done,
by defining the selection criteria that we drew from the TableEdu 4.0 application
installed on the Anatomage table. We first choose eight software based on these cri-
teria, and by Benchmarking, we have reduced this list to two software. In addition to
that, many annotations were added to the 3D reconstructions done on the Anatomage
table using images taken by different equipment. However, further investigations must
be done, using these results, to both create a new DICOM file by a programming
language and a new DICOM file manipulation software.

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