Machine learning is changing the way healthcare professionals diagnose and treat diseases. And if there is a medical field in which this is particularly evident, it is digital pathology.
Computer vision models can now detect diseases such as diabetic retinopathy or breast cancer with remarkable accuracy. AI is able to recognize subtle differences between normal and abnormal tissue. It can go through a sample and check every single cell for signs of cancer in a fraction of the time that a pathologist would need. AI models can also identify patterns in medical images that are too complex for the human eye to notice.
However, in order for these models to be accurate and reliable, they must be trained on large datasets of annotated digital pathology samples.
The process usually looks something like this:
Step 1: Labeling your data with semi-automatic segmentation tools
Step 2: Training an AI classification and instance segmentation model
Step 3: Using the model for automated analysis of your new data
In the example above, we trained a model to segment red blood cells and leukocytes. We can use it to analyze histological slides and get RBC-to-leukocyte ratio in seconds. With some additional tweaks, the model can detect blood cell formation patterns.
While this sort of task is surprisingly easy to complete with digital pathology annotation software, there are many things that can go wrong.
This article outlines the best practices and challenges associated with annotating digital pathology images for AI projects.
Let’s start with some potential obstacles that you should be aware of as a pathologist.
Pathology images can be very complex and may contain a wide range of different structures and patterns. This can make it difficult to accurately label and annotate the samples, as it requires a deep understanding of the underlying biology and pathology.
Common challenges of annotating tissue samples and training AI models for digital pathology include:
Thankfully, you can address all of these problems with careful planning and the right tools.
Here are some best practices for working with digital pathology images:
Determine what you are going to analyze at the very beginning of the project. To detect and measure the size of a granule, you might want to decide on polygons or bounding box annotations. But if we need to track the movement of bacteria, keypoint skeletons may produce more accurate models.
Some annotation classes are suitable for measuring growth or trajectory while others are better suited for tasks such as object classification.
It is also important to establish some rules for labeling similar structures. For instance, you can create one class for a specific cell type but use additional attributes such as “normal”, “abnormal”, “malignant”, etc. Alternatively, in some scenarios, it might be better to disregard class attributes and create“normal cell” and “cancer cell” as two separate classes. It is up to you, but make sure to stick to one method.
In V7 you can choose your annotation classes, labels, and attributes while setting up a new dataset annotation project. Then you can block other users from creating new label types on their own.
This can help you control the annotation process and ensure that your data is consistent and valid. Just remember to write an instruction for your annotators and explain which objects need labeling with and with labels.
Pathologists may have different interpretations of the same slide. It is important to resolve any discrepancies to ensure that the dataset is of high quality. Consensus stages and reviews can help to identify and address any disagreements about the labels for a given tissue sample. They can also help to identify any biases.
For instance, you can decide what level of annotation overlap (for instance, based on Intersection Over Union) is acceptable. The same slide is then labeled by multiple annotators who cannot see each other's annotations. The annotations are then compared to determine the level of agreement between the annotators. If the level of agreement is below the acceptable threshold, the annotations are reviewed by a senior pathologist or a panel of experts.
Consensus stages can also be helpful for testing the performance of AI models. During later iterations of your project, you can measure the level of agreement between the model's predictions and the expert annotations. This information will give you valuable insights and help you identify any potential issues or areas for improvement.
Annotating a tissue sample point by point is very time-consuming. Fortunately, an auto-annotation tool can be used to quickly outline regions of interest. These tools are typically based on convolutional neural networks designed to recognize patterns in images. While they won’t classify tissues or objects without some additional training, they do recognize common shapes and patterns out of the box.
For instance, a generic auto-annotation can automatically detect where one cell type ends and another begins. We can then map these regions to specific classes and add some additional attributes if necessary.
Later on, this tool can be trained to recognize and highlight specific structures, such as tissue-folds in histopathological samples. All we need is an initial training set based on “generic” auto-annotations.
Some annotation tools are not able to handle large files or medical imaging formats. For example, you may experience slow loading times or other performance issues when working with large files. You may be unable to open or view certain types of medical imaging files, especially multichannel slides, Z-stack or time lapse series.
A good annotation platform should let you use video annotation features (such as frame interpolation) for time-lapse microscopy. It is also important that your training data engine supports SVS technology. By breaking a file into tiles, these viewers and platforms let you view and annotate images at different zoom levels without loss of resolution
By choosing a tool that is specifically designed to handle medical imaging formats, you can avoid many technical issues and ensure that you are able to annotate your digital pathology slides efficiently.
Still, with some tissue samples you may want to split one slide into multiple images for convenience. In V7, you can automatically crop slides and generate new datasets based on individual tiles with webhooks.
Most AI platforms require lots of data for training an accurate model. And some pathology samples may need to be pre-processed, normalized, and cleaned before the annotation process even starts. That’s why coming up with proof of concept machine learning pipelines can be so challenging.
But why start from scratch when you can build on what's already there?
If you want to test if AI can detect specific cells, bacteria, or microvascular changes it is best to try it out on existing open datasets for computer vision tasks. You can browse open-source digital pathology files to compare different annotation techniques or labels used for specific cases. With a V7 account, you can also import them, make adjustments, and train your own models. In some cases, you can create cell detection or tissue segmentation models with as little as 10 slides.
Machine learning has been a key driving force in the development of digital pathology. The advancements in computer vision have helped to reduce the time and cost of research, diagnosis, and treatment. By combining digital microscopy and artificial intelligence, clinicians and researchers can now analyze slides and detect features of interest faster than ever.
But, AI models are only as good as the data they are trained on. So, the quality of the data is paramount.
That’s why the proper annotation of digital pathology images is becoming an increasingly important skill.
Automation tools, such as Auto-Annotate, can help you to speed up the labeling process but it is also essential to pay attention to:
By following the guidelines from this article and using the right software, you can ensure that your project is successful.
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