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DO-U-Net for Segmentation and Counting

Applications to Satellite and Medical Images

Part of the Lecture Notes in Computer Science book series (LNISA,volume 12080)

Abstract

Many image analysis tasks involve the automatic segmentation and counting of objects with specific characteristics. However, we find that current approaches look to either segment objects or count them through bounding boxes, and those methodologies that both segment and count struggle with co-located and overlapping objects. This restricts our capabilities when, for example, we require the area covered by particular objects as well as the number of those objects present, especially when we have a large amount of images to obtain this information for. In this paper, we address this by proposing a Dual-Output U-Net. DO-U-Net is an Encoder-Decoder style, Fully Convolutional Network (FCN) for object segmentation and counting in image processing. Our proposed architecture achieves precision and sensitivity superior to other, similar models by producing two target outputs: a segmentation mask and an edge mask. Two case studies are used to demonstrate the capabilities of DO-U-Net: locating and counting Internally Displaced People (IDP) tents in satellite imagery, and the segmentation and counting of erythrocytes in blood smears. The model was demonstrated to work with a relatively small training dataset, achieving a sensitivity of 98.69% for IDP camps of the fixed resolution, and 94.66% for a scale-invariant IDP model. DO-U-Net achieved a sensitivity of 99.07% on the erythrocytes dataset. DO-U-Net has a reduced memory footprint, allowing for training and deployment on a machine with a lower to mid-range GPU, making it accessible to a wider audience, including non-governmental organisations (NGOs) providing humanitarian aid, as well as health care organisations.

Keywords

  • Convolutional neural networks
  • U-Net
  • Segmentation
  • Counting
  • Satellite imagery
  • Blood smear

1 Introduction

Over recent years, the volumes of data collected across all industries globally have grown dramatically. As a result, we find ourselves in an ever greater need for fully automated analysis techniques. The most common approaches to large scale data analysis rely on the use of supervised and unsupervised Machine Learning, and, increasingly, Deep Learning. Using only a small number of human-annotated data samples, we can train models to rapidly analyse vast quantities of data without sacrificing the quality or accuracy compared with a human analyst. In this paper, we focus on images - a rich datatype that often requires rapid and accurate analysis, despite its volumes and complexity. Object classification is one of the most common types of analysis undertaken. In many cases, a further step may be required in which the classified and segmented objects of interest need to be accurately counted. While easily performed by humans, albeit slowly, this task is often non-trivial in Computer Vision, especially in the cases where the objects exist in complex environments or when objects are closely co-located and overlapping. We look at two such case studies: locating and counting Internally Displaced People (IDP) shelters in Western Afghanistan using satellite imagery, and the segmentation and counting of erythrocytes in blood smear images. Both applications have a high impact in the real world and are in a need of new rapid and accurate analysis techniques.

1.1 Searching for Shelter: Locating IDP Tents in Satellite Imagery

Over 40 million individuals were believed to have been internally displaced globally in 2018 [1]. Afghanistan is home to 2,598,000 IDPs displaced by conflict and violence, with the numbers growing by 372,000 in the year 2018 alone. In the same year, an additional 435,000 individuals were displaced due to natural disasters, 371,000 of whom were displaced due to drought.

The internally displaced population receive aid from various non-governmental organisations (NGOs), to prevent IDPs from becoming refugees. The Norwegian Refugee Council (NRC) is one such body, providing humanitarian aid to IDPs across 31 countries, assisting 8.5 million people in 2018 [2]. In Afghanistan, the NRC has been providing IDPs with tents as temporary living spaces. Alcis is assisting the NRC with the analysis of the number, flow, and concentration of these humanitarian shelters, enabling valuable aid to be delivered more effectively.

Existing Methods. In the past, Geographical Information System (GIS) Technicians relied mostly on industry-standard software, such as ArcGIS, for the majority of their analysis. These tools provide the user with a small number of built-in Machine Learning algorithms, such as the popularly used implementation of the Support Vector Machine (SVM) algorithm [3]. These generally involve a time consuming, semi-automated process, with each step being revisited multiple times as manual tuning of the model parameters is required. The methodology does not allow for batch processing as all stages must be repeated with human input for each image. An example of the ArcGIS processFootnote 1 used by GIS technicians is:

  1. 1.

    Manually segment the image by selecting a sample of objects exhibiting similar shape, spectral and spatial characteristics.

  2. 2.

    Train the image classifier to identify other examples similar to the marked sample, using a built-in machine learning model (e.g. SVM).

  3. 3.

    Identify any misclassified objects and repeat the above steps.

More recently, many GIS specialists have begun to look towards the latest techniques in Data Science and Big Data analysis to create custom Machine Learning solutions. A review paper by Quinn et al. in 2018 [4] weighed up the merits of Machine Learning approaches used to segment and count both refugee and IDP camps. Their work used a sample of 87,123 structures; a magnitude which was required for training using their approach and was seen as a limitation. Quinn et al. used the popular Mask R-CNN [5] segmentation model to analyse their data; a model using a Region Proposal Network to simultaneously classify and segment images. This yielded an average precision of 75%, improving to 78% by applying a transfer learning approach.

1.2 Counting in Vein: Finding Erythrocytes in Blood Smears

The counting of erythrocytes, or red blood cells, in blood smear images, is another application in which one must count complex objects. This is an important task in exploratory and diagnostic medicine, as well as medical research. An average blood smear imaged using a microscope, contains several hundred erythrocytes of varying size, many of which are overlapping, making an accurate manual count both difficult and time-consuming.

Existing Methods. While only a small number of analyses were able to successfully perform an erythrocyte count, Tran et al. [6] have achieved a counting accuracy of 93.30%. Their technique relied on locating the cells using the SegNet [7] network. SegNet is an encoder-decoder style FCN architecture producing segmentation masks as its output. Due to the overlap of erythrocyte cells, they performed a Euclidean Distance Transform on the binary segmentation masks to obtain the location of each cell using a connected component labelling algorithm. A work by Alam and Islam [8] proposes an approach using YOLO9000 [9]; a network using a similar approach to Mask R-CNN, to locate elliptical bounding regions that roughly correspond to the outer contours of the cells. Using 300 images, each containing a small number of erythrocytes, for training, they achieve an accuracy of 96.09%. Bounding boxes acted as ground-truth for Alam and Islam, as opposed to segmentation masks used by Tran et al.

2 Data Description

2.1 Satellite Imagery

Working on the ground, the NRC identified areas within Western Afghanistan with known locations of IDP camps. Through their relationship with Maxar [10], Alcis has access to satellite imagery covering multiple camps, in a range of different environments. Figure 1 shows a section of a camp in Qala’e’Naw, Badghis.

This work uses imagery collected by the WorldView-2 and WorldView-3 satellites [11], by their operator and owner Maxar. WorldView-2 has a multispectral resolution of 1.85 m, while the multispectral resolution of WorldView-3 is 1.24 m [12], allowing tents of approximately 7.5 m long and 4 m wide to be resolved. The WorldView-2 images were captured on either 05/01/19 (DD/MM/YY) or 03/03/19, with the WorldView-3 images captured on 12/03/19. A further set of images, observed between 08/08/18 and 23/09/19 by WorldView-3, became available for some locations. This dataset can be used to show evolution in the camps during this period, allowing for a better understanding of the changes undergone in IDP camps. Due to the orbital position of the satellite, images observed at different times have varying resolutions, as well as other properties, due to differences in viewing angle and atmospheric effects.

Training Data. We developed DO-U-Net using a limited number of satellite images, obtained over a very limited time, with a nearly identical pixel scale. Each tent found in the training imagery has been marked with a polygon, using a custom Graphical User Interface (GUI) tool developed by Alcis. This has been done for a total of 6 images, covering an area of approximately 15 km\(^2\) and containing 5,178 tents. Incidentally, this makes our training dataset nearly 17 times smaller than that used by Quinn et al. in their analysis.

The second satellite dataset includes imagery of varying quality and resolution, providing an opportunity to develop a scale-invariant version of our model. We used 3 additional training images, distinct from the original dataset, to train our scale-invariant DO-U-Net. These images contained 2,338 additional tents, in an area of around 130 km\(^2\), giving a total of 7,516 tents in over 140 km\(^2\).

2.2 Blood Smear Images

We used blood smear images from the Acute Lymphoblastic Leukemia (ALL) Image Database for Image ProcessingFootnote 2. These images were captured using an optical laboratory microscope, with magnification ranging from 300–500\(\times \), and a Canon PowerShot G5 camera. We used the ALL_IDB1 dataset, comprised of 108 images taken during September 2005 from both ALL and non-ALL patients. An example blood smear image from an ALL patient can be seen in Fig. 2.

Training Data. We selected 10 images from the ALL_IDB1 dataset to be used as training data. These images are representative of the diverse nature of the entire dataset, including the varying microscope magnifications and backgrounds. Of the images used, 3 belong to ALL patients, with the remaining 7 images coming from non-ALL patients. Similarly to the IDP camp dataset, all erythrocytes in the training data have been manually labelled with a polygon using our custom GUI tool. In the images belonging to ALL patients, a total of 1,300 erythrocytes were marked. A further 3,060 erythrocytes were marked in the images belonging to non-ALL patients, giving a total of 4,360 erythrocytes in the training data.

The training data does not distinguish between typical erythrocytes and those with any forms of morphology - of the 4,360 erythrocytes, just 106 display a clear morphology. The training data also does not contain any annotation for leukocytes. Instead, our focus is on correctly segmenting and counting all erythrocytes in the images.

Fig. 1.
figure 1

Left: An IDP camp in Badghis, Afghanistan. NRC tents are clearly visible due to their uniform size and light colour. Right: The manually created ground-truth annotation for the image.

Fig. 2.
figure 2

Left: An image of a blood smear from an Acute Lymphoblastic Leukemia (ALL) patient. Right: The manually created ground-truth annotation for the image. The images also contain lymphocytes, which are not marked in the training data.

3 Methodology

Of late, several very advanced and powerful Computer Vision algorithms have been developed, including the popular Mask R-CNN [5] and YOLO [9] architectures. While their performance is undoubtedly impressive, they rely on a large number of images to train their complex networks, as highlighted by Quinn et al. [5]. More recently, many more examples of FCN have been developed, including SegNet [7], DeconvNet [13] and U-Net [14], with the latter emerging as arguably one of the most popular encoder-decoder based architectures. Aimed at achieving a high degree of success even with sparse training datasets and developed to tackle biological image segmentation problems, it is a clear starting block for our architecture.

3.1 U-Net

The classical U-Net, as proposed by Ronneberger et al. has revolutionised the field of biomedical image segmentation. Similarly to other encoder-decoder networks, U-Net is capable of producing highly precise segmentation masks. What differentiates it from Mask R-CNN, SegNet and other similar networks is its lack of reliance on large datasets [14]. This is achieved by the introduction of a large number of skip connections, which reintroduce some of the early encoder layers into the much deeper decoder layers. This greatly enriches the information received by the decoder part of the network, and hence reduces the overall size of the dataset required to train the network.

We have deployed the original U-Net on our dataset of satellite images of IDP camps in Western Afghanistan. While we were able to produce segmentation masks that very accurately marked the location of the tents, the segmentation masks contained significant overlaps between tents, as seen in Fig. 3. This overlap prevents us from carrying out an automated count, despite using several post-processing techniques to minimise the impact of these overlaps. The most successful post-processing approaches are shown in Fig. 3. The issues encountered with the classical U-Net have motivated our modifications to the architecture, as described in this work.

Fig. 3.
figure 3

a: Sample segmentation mask in which some tent segmentations are seen to overlap. b: Sobel filtered image. c: Local entropy filtered image. d: Otsu filtered image. e: Image with contour ellipses applied. f: Image with gradient morphology applied. g: Eroded image. h: Tophat filtered image. i: Blackhat filtered image.

3.2 DO-U-Net

Driven by the need to reduce overlap in segmentation masks, we modified the U-Net architecture to produce dual outputs, thus developing the DO-U-Net. The idea of a contour aware network was first demonstrated by the DCAN architecture [15]. Based on a simple FCN, DCAN was trained to use the outer contours of the areas of interest to guide the training of the segmentation masks. This led to improved semantic and instance segmentation of the model, which in their case, looked at non-overlapping features in biomedical imaging.

With the aim of counting closely co-located and overlapping objects, we are predominantly interested in the correct detection of individual objects as opposed to the exact precision of the segmentation mask itself. An examination of the hidden convolutional layers of the classical U-Net showed that the penultimate layer of the network extracts information about the edges of our objects of interest, without any external stimulus. We introduce a secondary output layer to the network, targeting a mask segmenting the edges of our objects. By subtracting this “edge” mask from the original segmentation mask, we can obtain a “reduced” mask containing only non-overlapping objects.

As our objective was to identify tents of fixed scale in our image dataset, we were able to simplify the model considerably. This reduced the computational requirements in training of the model, allowing not only for much faster development and training but also opening the possibility of deploying the algorithm on a dataset covering a large proportion of the total area of Afganistan, driven by our commercial requirements.

Architecture. Starting with the classical U-Net, we reduce the number of convolutional layers and skip connections in the model. Simultaneously, we minimised the complexity of the model by looking at smaller input regions of the images, thus minimising the memory footprint of the model. We follow the approach of Ronneberger et. al. by using unpadded convolutions throughout the network, resulting in a model with smaller output masks (100 \(\times \) 100 px) corresponding to a central region of a larger (188 \(\times \) 188 px) input image region. DO-U-Net uses two, independently trained, output layers of identical size. Figure 4 shows our proposed DO-U-Net architecture. The model can also be found in our public online repositoryFootnote 3. Examples of the output edge and segmentation masks, as well as the final “reduced” mask, can be seen in Figs. 6 and 7. With the reduced memory footprint of our model, we can produce a “reduced” segmentation mask for a single 100 \(\times \) 100 px region in 3 ms using TensorFlow 2.0 with Intel i9-9820X CPU and a single NVIDIA RTX 2080 Ti GPU setup.

Fig. 4.
figure 4

The DO-U-Net architecture, showing two output layers that target the segmentation and edge masks corresponding to the training images.

Training. The large training images were divided such that no overlap exists between the regions corresponding to the target masks, using zero-padding at the image borders. We train our model against both segmentation and edge masks. The edges of the mark-up polygons, annotated using our custom tool, were used as the “edge” masks during training. Due to the difference in a pixel size of tents and erythrocytes, the edges were taken to span 2 px and 4 px wide respectively in these case studies.

As our problem deals with segmentation masks covering only a small proportion of the image (<1% in some satellite imagery), the choice of a loss function was a very important factor. We use the Focal Tversky Index, which is suited for training with sparse positive labels compared to the overall area of the training data [16]. Our best result, obtained using the Focal Tversky loss function, gave an improvement of 5% in the Intersect-over-Union (IoU) value compared to the Binary Cross-Entropy loss function, as used by Ronneberger et al. [14]. We found the training to behave most optimally when the combined loss function for the model was heavily weighted toward the edge mask segmentation. Here, we used a 10%/90% split for the object and edge mask segmentation respectively.

Counting. As the resulting “reduced” masks produced by our approach do not contain any overlaps, we can use simple counting techniques, relying on the detection of the bounding polygons for the objects of interest. We apply a threshold to remove all negative values from the image, which may occur due to the subtractions. We then use the Marching Squares Algorithm implemented as part of Python’s skimage.measure image analysis library [17].

Scale-Invariant DO-U-Net. In addition to the simple DO-U-Net, we propose a scale-invariant version of the architecture with an additional encoder and decoder block. Figure 5 shows the increased depth of the network as is required to capture the generalised model of our objects in the scale varying dataset. The addition of extra blocks resulted in a larger input layer of 380 \(\times \) 380 px, corresponding to a segmentation mask of 196 \(\times \) 196 px.

Fig. 5.
figure 5

Scale-Invariant DO-U-Net, redesigned to work with datasets containing objects of variable scale.

4 Results

4.1 IDP Tent Results

Using our DO-U-Net architecture, we were able to achieve a very significant improvement in the counting of IDP tents compared to the popularly used SVM classifier available in ArcGIS. However, due to the manually intensive nature of the ArcGIS approachFootnote 4, we were only able to directly compare a single test camp, located in the Qala’e’Naw region of the Badghis Province. This area contains 921 tents as identified in the ground-truth masks. Using DO-U-Net, we achieved a precision of 99.78% with a sensitivity of 99.46%. Using ArcGIS, we find a precision of 99.86% and a significantly lower sensitivity of 79.37%. Sensitivity, or the true positive rate, measures the probability of detecting an object and is, therefore, the most important metric for us as we aim to locate and count all tents in the region. The scale-invariant DO-U-Net achieved a precision of 98.48% and a sensitivity of 98.37% on the same image.

Fig. 6.
figure 6

Left: Segmentation mask produced for NRC tents in a camp near Qala’e’Naw. Centre: Edges mask produced for the same image. Right: The final output mask.

We also apply DO-U-Net to a larger dataset of five images containing a total of 3,447 tents and find an average precision of 97.01% and an average sensitivity of 98.68%. Similarly, we tested the scale-invariant DO-U-Net using 10 images with varying properties and resolutions containing a total of 5,643 tents. Here, the average precision was reduced to 91.45%, and the average sensitivity dropped to 94.66%. This result is not surprising as, on inspection, we find that without the scale constraints the resulting segmenting masks are contaminated with other structures of similar properties to NRC tents. We also find that, without scale constraints, NRC tents which are partially covered e.g. with tarpaulin may be missed or only partially segmented. Our DO-U-Net and scale-invariant DO-U-Net sensitivities of 98.68% and 94.66% respectively are very strong results when compared to the existing literature.

Fig. 7.
figure 7

Left: Segmentation mask produced for a blood smear of an ALL patient. Centre: Edges mask produced for the same image. Right: The final output mask.

4.2 Erythrocyte Results

To validate the performance of DO-U-Net at counting erythrocytes, we use 3 randomly selected blood smear images from ALL patients and a further 5 selected images from non-ALL patients. While randomly selected, the images are representative of the entire ALL_IDB1 dataset. On a total of 2,775 erythrocytes, as found in these 8 validation images, DO-U-Net achieved an average precision of 98.31% and an average sensitivity of 99.07%.

Fig. 8.
figure 8

Top: Blood smear images of overlapping cells. Bottom: Segmentation masks produced by DO-U-Net. Left: An overlapped cell is counted twice when the “edges” from neighbouring cells overlap and break up the cell. Centre: A cell is missed due to an incomplete edge mask. Right: An uncertainty in the order of the cell overlap leads to the intersect between two cells being counted as an additional cell.

Whilst our proposed DO-U-Net is extremely effective at producing image and edge segmentation masks, as demonstrated in Fig. 7, we do note that the obtained erythrocyte count may not always match the near-perfect segmentation. Figure 8 shows examples of the three most common issues found to occur in the final “reduced” masks. These mistakes arise largely due to the translucent nature of erythrocytes and the difficulty in differentiating between a cell which is overlapping another and a cell which is overlapped. While these cases are rare, this demonstrates that further improvements can be made to the architecture.

4.3 Future Work

Our current model has been designed to segment only one type of object, which is a clear limitation of our solution. As an example, the blood smear images from the ALL-IDP1 dataset contain normal erythrocytes as well as two clear types of morphology: burr cells and dacryocytes. These morphologies may be signs of disease in patients, though burr cells are common artefacts, especially known to occur when the blood sample is aged. It is therefore important to not only count all erythrocytes, but to also differentiate between their various morphologies. While our general theory can be applied to identifying different types of object, further modifications to our proposed DO-U-Net would be required.

Table 1. Summary of results for DO-U-Net, when tested on our two satellite imagery datasets and the ALL_IDB1 dataset.

5 Conclusion

We have proposed a new approach to segmenting and counting closely co-located and overlapping objects in complex image datasets. For this, we developed DO-U-Net: a modified U-Net based architecture, designed to produce both a segmentation and an “edge” mask. By subtracting the latter from the former, we can locate and spatially separate objects of interest before automatically counting them. Our methodology was successful on both of our case studies: locating and counting IDP tents in satellite imagery, and the segmentation and counting of erythrocytes in blood smear images. In the first case study, DO-U-Net increased our sensitivity by approximately 20% compared to a popular ArcGIS based solution, achieving an average sensitivity of 98.69% for a dataset of fixed spatial resolution. Our network went on to achieve a precision of 91.45% and a sensitivity of 94.66% on a set of satellite images with a varying resolution and colour profiles. This is an impressive result when compared to Quinn et al. who achieved a precision of 78%. We also found DO-U-Net to be extremely successful at segmenting and counting erythrocytes in blood smear images, achieving a sensitivity of 99.07% for our test dataset. This is an improvement of 6% over the results found by Tran et al. who used the same training dataset, and 3% over Alam and Islam who used a comparable set of images, giving us a near-perfect sensitivity when counting erythrocytes. The results are summarised in Table 1.

Notes

  1. 1.

    Details of the process have been provided by Alcis.

  2. 2.

    Provided by the Department of Information Technology at Università degli Studi di Milano, https://homes.di.unimi.it/scotti/all/.

  3. 3.

    https://github.com/ToyahJade/DO-U-Net.

  4. 4.

    Results found using ArcGIS methodology can be found at https://storymaps.arcgis.com/stories/d85e5cca27464d97ad4c1bad3da7f140.

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Acknowledgements

We thank Harry Robson, GIS Analyst at Alcis Holdings Ltd., for industry knowledge shared and for performing post-processing in ArcGIS. We would also like to show our gratitude to Richard Brittan, Tim Buckley and the Alcis team for sharing insight with us during the course of this research.

We are also immensely grateful to the Department of Information Technology at Università degli Studi di Milano for providing the ALL_IDB1 dataset from the Acute Lymphoblastic Leukemia Image Database for Image Processing.

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Overton, T., Tucker, A. (2020). DO-U-Net for Segmentation and Counting. In: Berthold, M., Feelders, A., Krempl, G. (eds) Advances in Intelligent Data Analysis XVIII. IDA 2020. Lecture Notes in Computer Science(), vol 12080. Springer, Cham. https://doi.org/10.1007/978-3-030-44584-3_31

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