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How to debug a synapse classifier with webKnossos

Interview with Valentin Pinkau

Today, we will have a chat with one of our colleagues: Valentin Pinkau. Valentin has been working as a machine learning engineer at scalable minds for 5 years. As an experienced data scientist specializing in connectomics, he has some interesting insights to share.

What is your role at scalable minds?

As a data scientist, I continuously work on our products, talk to collaborators about their needs, handle deadlines, and train machine learning models. This means sometimes training a classifier, debugging it iteratively and so on, and sometimes building data processing pipelines.

Valentin Pinkau, machine learning engineer at scalable minds.

What do you like most about your work here?

The fact that we support researchers in neuroscience and life sciences, which is a meaningful purpose. I also find my tasks exciting: training models, working with machine learning and diving deep into the wonderful data.

I heard you are the synapses specialist. Could you describe what your work on synapses has been in the last months?

Sure. First a little bit of context: as you know, one of our specializations is connectomics, meaning, we reconstruct neurons from volume electron microscopy data. One crucial element about this reconstruction is to identify where the neurons “talk” to one another. This means we have to find the synapses in the EM data given to us by collaborators and reconstruct which neurons are the pre and postsynaptic partners, to then build a connectome matrix. We also extract further information, which can be relevant to biologists, like synapse types (shaft, soma, spinehead, etc).

Following an axon (in red) until a spinehead synapse. Reconstruction and animation by scalable minds.

So how do you teach your model to detect such things? What are the steps you have to make to obtain this information and which tools do you use?

It all starts with what we call the “ground truth”: bounding boxes of volume EM data annotated by biologists.

Ground truth: EM images on which scientists annotated the synapses, mitochondrias (orange) and vesicles (green). Check out the published data here.

As you can see in this image, some scientists (Motta et al. 2019) annotated the synaptic clefts in the EM images (red, brown), along with mitochondrias (orange) and vesicles (green). They also indicated the synapse types: spine-head or dendritic shaft synapse. The scientists generate their training data using webKnossos, which is great to manually and collaboratively annotate EM data, and then simply send me a link to the annotated dataset. Based on this, I train my machine learning model with Voxelytics to detect such information, using a fully convolutional residual Unet.

Now that I have a trained synapse classifier, I can run the model on other datasets, or rather, the dataset that needs an automated synapse detection. This approach is called supervised learning and is a standard practice for these instance segmentation problems.

The images below show the prediction results of our synapse classifier on a new dataset: the spine-head synapses are highlighted in red, the non-spine-head synapses in green, the mitochondrias in pink and the vesicles in blue.

Prediction results: spine-head synapses are highlighted in red, the non-spine-head synapses in green, the mitochondrias in pink and the vesicles in blue.

That sounds amazing. So you run your ML model on any EM dataset, obtain a prediction and the work is done?

Not exactly. The next step is to evaluate how well the model performed, meaning, how many of the predicted synapses are actually synapses. This is a challenging step, for which webKnossos’ project management features are essential.

Subset with the synapses annotated as 3-nodes skeletons by the scientists (ground truth for evaluation).

First, I execute our AI toolbox Voxelytics to detect where physical contacts exist between pairs of neurons (a physical contact won’t necessarily mean that there is a synapse). If a physical contact exists where the prediction indicates a synapse, a three-point annotation (pre, post, cleft) will be created. We visualize these annotations in webKnossos as skeletons.

To evaluate the model, I run the predictions on an evaluation box and automatically compare my 3-point annotation with a ground-truth 3-point annotation done by the biologists. In some cases, I will have a look at the detected mistakes to try to understand how they happened.

Finally, I discuss the result of the comparison with the scientists in order to decide how to proceed: e.g. fix errors in the ground truth, iterate on the model if it is not good enough, or run it on the whole dataset. Once the synapse detection has run on the complete dataset, I can visualize them on webKnossos (despite the huge size of the dataset) and share a link with the scientists.

And how can webKnossos help you debug the synapse classifier?

Well, debugging the synapse classifier means going through the evaluation process and understanding how and when mistakes happen so that I can improve the classifier until it is good enough to run on the whole dataset.

For this, webKnossos is an amazing tool: it allows me to visualize the ground truth and my predictions (as skeletons or as volume annotations) as overlapping layers, which can be very handy for the evaluation step. I can jump to the different synapse locations using the right sidebar and inspect the synapse predictions to understand the errors.

webKnossos’ interface: on the right, list of 3-points annotations (click on a tree to jump to the synapse’s location).

Let’s take an example: imagine there is a synapse in the ground truth but none in my prediction. To find out what happened, I go through the different steps of the process in webKnossos. I might realize that the synapse was detected and appeared in my prediction layer. However, the neuron segmentation might have been wrong at this location and did not indicate a physical contact. Due to the missing contact, the synapse would not be marked as a 3-point prediction and does not appear in the result.

Overview of the training and evaluation process. Ground truth, volume predictions, segmentations, 3-points prediction, and 3-points ground truth are all visible in webKnossos and allow to trace back where the classifier is wrong during the evaluation process.

Now, I know that I cannot fix this error in the synapse detection, but need to go back to the neuron reconstruction segmentation. With webKnossos, this is as easy as activating additional layers, such as the neuron segmentation and the CNN predictions of the reconstruction.

I understand debugging a synapse classifier is quite a challenge. Thank you Valentin for sharing your insights!

We hope these few lines helped you with your research, informed you, or simply interested you. As you can see, webKnossos is a great open-source tool for electron microscopy image analysis and has become indispensable to scalable minds’ data scientists. Follow us on Twitter to be kept in the loop about webKnossos’ continuous improvements!

Image credits:

  • Predictions, segmentations and meshes by scalable mind
  • Raw EM data, Mouse Cortex by Motta et al., Science, 2019

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