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Healthc Inform Res > Volume 27(2); 2021 > Article
Sharmin, Chow, Dong, and Milos: Histoscope: A Web-Based Microscopy Tool for Oral Histology Education



Histology, the study of tissue structure under a microscope, is one of the most essential yet least engaging topics for health professional students. Understanding tissue microanatomy is crucial for students to be able to recognize cellular structures and follow disease pathogenesis. Traditional histology teaching labs rely on light microscopes and a limited array of slides, which inhibits simultaneous observation by multiple learners, and prevents in-class discussions. We have developed an interactive web-based microscopy tool called “Histoscope” for oral histology in this context.


Good quality microscope slides were selected for digital scanning. The slides were scanned with multiple layers of z-stacking, a method of taking multiple images at different focal distances. The digital images were checked for quality and were archived on Histoscope. The slides were annotated, and self-assessment questions were prepared for the website. Interactive components were programmed on the website to mimic the experience of using a real light microscope.


This web-based tool allows users to interact with histology slides, replicating the experience of observing and manipulating a slide under a real microscope. Through this website, learners can access a broad array of digital oral histology slides and self-assessment questions.


Incorporation of Histoscope in a course can shift traditional teacher-centered histology learning to a collaborative and student-centered learning environment. This platform can also provide students the flexibility to study histology at their own pace.

I. Introduction

Histology, the study of tissue structure under a microscope, has always been the principal approach to the structural analysis of living organisms at the cellular level. Understanding tissue microanatomy is essential to train medical, dental, and other health professional students to recognize cellular structures, comprehend the structure-function relationship of cells and tissues, and follow disease pathogenesis. However, this branch of science has been described as one of the least engaging topics by health professional students [1]. The traditional method of teaching histology relies on light microscopes, which does not allow simultaneous observation by multiple people, prevents interactive in-class discussions, and thus fails to motivate students [2].
At the School of Dentistry at the University of Alberta, students extensively study oral histology to learn about teeth and surrounding oral structures, their development, and developmental anomalies. Besides regular didactic lectures, students attend histology lab sessions in which they share a limited number of light microscopes and glass slides to view tooth and oral structures. The microscopic slides used for teaching are decades old, with some being extremely rare and irreplaceable.
A growing number of universities and medical schools worldwide are embracing digital slides as an alternative to traditional light microscopes [3,4]. The incorporation of virtual microscopy in histology and pathology courses has improved in-class teaching environments [3,5] and student performance [6]. The number of websites archiving digital histology slides is also growing internationally. For example, “The SecondLook” is a collection of histology slides developed by the University of Michigan [7]. “Oral Histology” created by the University of Kentucky College of Medicine contains a collection of annotated but low-resolution images of oral histology slides [8]. However, the existing web-based histology databases lack sufficient, high-quality resources from the oral cavity, which are critical for dentistry students. Most of the publicly available histology databases provide either annotated or non-annotated images without the ability to switch from one to the other, which does not allow learners to perform active memory recall after learning. Other drawbacks of the existing virtual microscopy websites are the quality of graphical resolution [9] and lack of z-axis information, which is essential for reconstructing the three-dimensional visualization of cellular structure [10]. Moreover, in most online sources, users cannot manipulate images to observe structural details. The few websites that provide the ability to zoom in and out permit users to expand a picture only at a predefined location. The inability to magnify any region of interest limits learners’ freedom to explore the histological section and restricts their curiosity, reducing the student-centeredness of their learning. Furthermore, the COVID-19 pandemic has moved most university teaching online, necessitating an alternative way to teach histology virtually yet in an interactive and engaging manner.
In this context, we have developed a web-based interactive microscopy tool called “Histoscope.” We have scanned our existing oral histological slides in high resolution and archived them on our website. The site allows users to interact with the digital slides and self-assess their knowledge of oral histology.

II. Methods

1. Slide Digitalization and Organization

The School of Dentistry has a collection of oral histology glass slides to teach histology labs with light microscopes. We curated those slides for quality and rarity and selected the best slides for whole-slide scanning using an Aperio Digital Slide Scanner (Leica Biosystems, Wetzlar, Germany). We chose the slides to represent the oral mucosa, oral structures, tooth, tooth development, and facial structure development. The slides were scanned with 25 layers of z-stacking, an image-processing method of taking multiple images at different focal distances and combining them to make a composite image. This technique, also known as focus stacking, is useful for capturing in-focus images of objects under high magnification as the depth of field decreases with magnification [11].
The histology glass slides were scanned under 20× or 40× magnification depending on the specimen’s size and the structural details required for teaching oral histology. The slides scanned under 40× magnification has a resolution of 0.247 microns per pixel (MPP); the resolution was 0.497 MPP for the slides scanned under 20× magnification. The image bit depth was 8 bits for all the digital slides.
Digital scans of the slides were further checked for quality and resolution, organized in groups, annotated, and archived on the Histoscope website under the Slide Gallery tab (Figure 1). Currently, the website contains 76 digital slides representing teeth and surrounding oral structures.

2. Self-Assessment Question Preparation

We prepared a series of questions (Figure 1D) which were incorporated into the website under the Self-Assessment tab. The questions are grouped to correspond to the Slide Gallery organization, so students can choose to test their knowledge of a specific area of the oral cavity. Currently, we have 35 image-labeling and structure-identification questions on our website, which are randomized each time a user takes the test.

3. Design and Layout of the Website

We aimed for a simple, responsive design with a minimum number of tabs and minimal text for easy navigation. For structural consistency, the title “Histoscope” and the background frame are kept visible on all pages (Figure 1A, 1B). The colors of the headings, tabs, and background were chosen for aesthetic harmony. The contents of the website are organized under six tabs. Digital slides are arranged in fifteen groups under the Slide Gallery tab (Figure 1A, 1B, Table 1). The Self-Assessment tab guides users to a series of questions to test their oral histology knowledge. The website also has an option for users to contact the authors and provide feedback for further improvement (Figure 1A).

4. Incorporation of Interactive Components

We designed Histoscope as an interactive microscopy tool. This interface’s primary goal is to mimic the experience of viewing slides through a real light microscope with the ability to manipulate and view various areas of the histological section, which is rare in the existing online histology databases. Our website was programmed with the Python programming language and uses Flask as a web framework, resulting in a dynamic platform capable of processing user requests and interacting with them accordingly. Users can load a digital slide of their choice in high resolution, rotate the slides as needed, toggle to full screen, and change the magnification in any mouse-pointed location. The digital slides on our website were scanned using the z-stacking technique to provide continuous z-axis information. Z-stacking allows for a greater depth of field and a unique ability to magnify a digital image at any given area and maintain a perfectly focused, high-resolution field-of-view (Figure 2). The slide viewer of the website provides an inset telescope box on the upper-right corner of the screen. When zooming in on fields of view, the inset shows a box outlined in red, delineating the exact position of the area being viewed on-screen with respect to the entire viewable field (Figure 2). After magnification, the user can navigate the magnified slide by grabbing the slide with a hand tool or by simply moving the red box in the inset (Figure 3). The slides are annotated by content experts to identify major structural components within a tissue section. Users can either “show” or “hide” the annotations, which allows them to self-test their learning (Figures 1C, 3).

III. Results

The completed website includes 76 high-quality and rare sections of the tooth, oral structures, and development of tooth and facial regions, which are not readily available in any public online databases. A complete list of all the digital slides incorporated into our slide gallery is shown in Table 1. The digital images were scanned using a focus stacking technology to mimic the experience of focusing through a real light microscope (Figure 2). We have included an option to show or hide annotations to enable users to perform active memory recall (Figure 3). Self-assessment questions on our website allow learners to self-test their knowledge on oral histology (Figure 1).

IV. Discussion

Computer-based technologies to teach histology have increased over the years [3,12,13]. Virtual microscopy has improved learners’ performance in many training programs [3,5,14]. Some known limitations of this technology are low graphics resolution and lack of z-axis information [9,10]. With Histoscope, we aimed to overcome the shortcomings of previous virtual histology databases and to create an interactive and dynamic platform to mimic the experience of using an actual light microscope. The incorporation of our web-based microscope will stimulate active learning and student engagement. Educational theories suggest that adults learn proficiently when they are fully engaged in learning [15]. Active engagement also helps develop critical thinking skills in adults [16]. The use of web-based microscopy in conjunction with an actual light microscope is supported by Mayer’s cognitive theory of multimedia learning, which states that using two or more of each of the modalities of delivery, presentation, and sensory systems will support effective learning [17]. We believe that Histoscope will complement traditional teaching with the light microscope and allow students to study histology at their own pace.


Conflict of interest

No potential conflict of interest relevant to this article was reported.


The authors sincerely thank Rehabilitation Robotics Lab, University of Alberta for developing our website, Histoscope.

Figure 1
Snapshots from the Histoscope website. (A, B) The contents of the website are organized under six tabs. (B) Digital slides are arranged in 15 groups under the “Slide Gallery” tab. (C) Snapshot of a slide showing the cross-section of a dental root. (D) Sample question from the Self-Assessment section of the website (D).
Figure 2
Application of z-stacking to provide in-focus images in high magnification. The slide collection of Histoscope was scanned using the z-stacking technique to allow the ability to magnify the digital slides and still get an entirely focused, high-resolution field-of-view. (A–C) A tissue section of a salivary gland, gradually magnified from low (A) to higher (B, C) magnification. The red box in the inset of each slide indicates the viewing area (arrow) and the scale bar at the bottom left shows the degree of magnification of the slide (arrow). The black box in the middle indicates the area that was being magnified. As the slides are viewed under higher magnification, the scale bar changes (from 2 mm to 100 μm), and the red box in the inset becomes smaller. Z-stacking enables the user to observe structural details under a higher magnification, mimicking the experience of using a light microscope.
Figure 3
Snapshot from the slide viewer of Histoscope. The user can activate the inset box on the upper-right corner of the slide viewer simply by the mouse pointer’s motion. While zooming in, the inset shows a box outlined in red, delineating the exact position of the area being viewed on-screen with respect to the entire viewable field. The control bar in the upper-left corner allows the user the zoom in, zoom out, rotate, and toggle to full-screen mood. “Show Labels” and “Hide Labels” allow users to show or hide the slide annotations.
Table 1
List of digital slides included in the “Slide Gallery” of Histoscope
Digital slides Properties

Scanning magnification Resolution (MPP) Pixel dimension
Cross section of crown
 Cross section of tooth crown (incisor) 20× 0.497 17,987 × 13,230
 Cross section of a tooth crown (premolar) 20× 0.497 35,975 × 28,613
 Cross section of occlusal surface (molar) 20× 0.497 21,585 × 19,294

Cross section of root
 Cross section of root I 40× 0.247 37,800 × 21,881
 Cross section of root II 40× 0.247 39,600 × 24,359
 Cross section of root III 40× 0.247 50,399 × 28,112
 Cross section of root, periodontal ligament, alveolar bone I 40× 0.247 54,000 × 49,764
 Cross section of root, periodontal ligament, alveolar bone II 40× 0.247 52,199 × 33,395
 Cross section of root, periodontal ligament, alveolar bone III 40× 0.247 50,399 × 39,356

Face development
 Cross section of embryo head (day 23) 20× 0.497 8,993 × 9,648
 Cross section of embryo head (developing tongue, palate) I 20× 0.497 10,792 × 13,916
 Cross section of embryo head (developing tongue, palate) II 20× 0.497 10,972 × 13,919
 Cross section of embryo head (developing tongue, palate) III 20× 0.497 12,591 × 15,064
 Cross section of embryo head (developing tongue, palate) IV 20× 0.497 10,792 × 15,729
 Cross section of embryo head (face development) I 20× 0.497 21,585 × 13,619
 Cross section of embryo head (face development) II 20× 0.497 21,585 × 13,045

 Longitudinal section of tooth, gingiva I 20× 0.497 55,762 × 28,349
 Longitudinal section of tooth, gingiva II 20× 0.497 52,164 × 28,198
 Longitudinal section of tooth, gingiva III 20× 0.497 57,561 × 25,626

Longitudinal tooth section
 Longitudinal ground section of tooth I 20× 0.497 34,176 × 15,701
 Longitudinal ground section of tooth II 20× 0.497 41,372 × 19,779
 Oblique section of tooth 20× 0.497 26,981 × 20,181
 Longitudinal ground section of tooth III 20× 0.497 34,176 × 18,663

Pulp stone
 Tooth cross section with pulp stone I 40× 0.247 48,600 × 33,743
 Tooth cross section with pulp stone II 40× 0.247 66,599 × 47,051

 Anterior palate I 40× 0.247 28,800 × 78,829
 Anterior palate II 40× 0.247 28,800 × 78,830
 Anterior palate III 40× 0.247 23,400 × 78,854
 Anterior palate IV 40× 0.247 23,400 × 78,856

Parotid gland
 Cross section of parotid gland I 20× 0.497 34,176 × 17,838
 Cross section of parotid gland II 40× 0.247 72,000 × 35,946
 Cross section of parotid gland III 40× 0.247 75,600 × 29,470
 Cross section of parotid gland IV 40× 0.247 63,000 × 27,881
 Cross section of parotid gland V 40× 0.247 54,000 × 37,850

Periodontal ligament
 Cross section of root, periodontal ligament, alveolar bone I 40× 0.247 54,000 × 49,764
 Cross section of root, periodontal ligament, alveolar bone II 40× 0.247 52,199 × 33,395
 Cross section of root, periodontal ligament, alveolar bone III 40× 0.247 50,399 × 39,356

Sublingual gland
 Cross section of sublingual gland I 40× 0.247 59,399 × 50,399
 Cross section of sublingual gland II 40× 0.247 52,199 × 50,928
 Cross section of sublingual gland III 40× 0.247 52,199 × 51,262

Submandibular gland
 Cross section of submandibular gland I 40× 0.247 46,800 × 40,366
 Cross section of submandibular gland II 40× 0.247 50,399 × 52,758
 Cross section of submandibular gland III 40× 0.247 55,800 × 46,282

Temporomandibular joint (TMJ)
 Cross section of adult TMJ I 20× 0.497 39,573 × 38,056
 Cross section of adult TMJ II 20× 0.497 41,372 × 40,021
 Cross section of adult TMJ III 20× 0.497 46,768 × 37,196
 Cross section of adult TMJ IV 20× 0.497 44,969 × 39,758

 Cross section of tongue I 20× 0.497 23,384 × 28,673
 Cross section of tongue II 20× 0.497 23,384 × 29,572
 Cross section of tongue III 20× 0.497 26,981 × 25,530
 Cross section of tongue IV 20× 0.497 25,183 × 21,910
 Cross section of tongue V 20× 0.497 23,384 × 28,255
 Cross section of tongue VI 40× 0.247 48,600 × 57,230
 Cross section of tongue VII 20× 0.497 35,975 × 18,656
 Cross section of tongue VIII 20× 0.497 34,167 × 16,192
 Cross section of tongue IX 20× 0.497 34,167 × 22,859

Tooth development
 Developing tooth germ I 20× 0.497 19,786 × 28,606
 Developing tooth germ II 20× 0.497 21,585 × 30,655
 Bell stage of tooth development I 20× 0.497 21,585 × 42,668
 Bell stage of tooth development II 20× 0.497 43,170 × 24,872
 Bell stage of tooth development III 20× 0.497 23,384 × 39,290
 Bell stage of tooth development IV 20× 0.497 26,981 × 44,779
 Bell stage of tooth development V 20× 0.497 23,384 × 41,182
 Bell stage of tooth development VI 20× 0.497 19,786 × 29,511

Tooth eruption
 Cross section of erupting tooth I 20× 0.497 26,981 × 27,831
 Cross section of erupting tooth II 20× 0.497 30,579 × 26,829
 Cross section of erupting tooth III 20× 0.497 30,579 × 24,025
 Cross section of erupting tooth IV 20× 0.497 30,579 × 26,253
 Cross section of erupting tooth V 20× 0.497 41,372 × 27,757
 Cross section of erupting tooth VI 20× 0.497 41,372 × 27,758
 Cross section of erupting tooth VII 20× 0.497 39,573 × 29,828
 Cross section of erupting tooth VIII 20× 0.497 39,573 × 29,826
 Cross section of erupting tooth IX 20× 0.497 37,774 × 21,687
 Cross section of erupting tooth X 20× 0.497 35,975 × 22,846
 Cross section of erupting tooth XI 20× 0.497 39,573 × 34,683
 Cross section of erupting tooth XII 20× 0.497 41,372 × 32,695


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