Real-time 3D fluorescence microscopy is crucial for the spatiotemporal analysis of live organisms, such as neural activity monitoring. The eXtended field-of-view light field microscope (XLFM), also known as Fourier light field microscope, is a straightforward, single snapshot solution to achieve this. The XLFM acquires spatial-angular information in a single camera exposure. In a subsequent step, a 3D volume can be algorithmically reconstructed, making it exceptionally well-suited for real-time 3D acquisition and potential analysis. Unfortunately, traditional reconstruction methods (like deconvolution) require lengthy processing times (0.0220 Hz), hampering the speed advantages of the XLFM. Neural network architectures can overcome the speed constraints but do not automatically provide a way to certify the realism of their reconstructions, which is essential in the biomedical realm. To address these shortcomings, this work proposes a novel architecture to perform fast 3D reconstructions of live immobilized zebrafish neural activity based on a conditional normalizing flow. It reconstructs volumes at 8 Hz spanning 512x512x96 voxels, and it can be trained in under two hours due to the small dataset requirements (50 image-volume pairs). Furthermore, normalizing flows provides a way to compute the exact likelihood of a sample. This allows us to certify whether the predicted output is in- or ood, and retrain the system when a novel sample is detected. We evaluate the proposed method on a cross-validation approach involving multiple in-distribution samples (genetically identical zebrafish) and various out-of-distribution ones.
Why Normalizing Flows Fail to Detect Out-of-Distribution Data
Detecting out-of-distribution (OOD) data is crucial for robust machine learning systems. Normalizing flows are flexible deep generative models that often surprisingly fail to distinguish between in- and out-of-distribution data: a flow trained on pictures of clothing assigns higher likelihood to handwritten digits. We investigate why normalizing flows perform poorly for OOD detection. We demonstrate that flows learn local pixel correlations and generic image-to-latent-space transformations which are not specific to the target image datasets, focusing on flows based on coupling layers. We show that by modifying the architecture of flow coupling layers we can bias the flow towards learning the semantic structure of the target data, improving OOD detection. Our investigation reveals that properties that enable flows to generate high-fidelity images can have a detrimental effect on OOD detection.
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- Award ID(s):
- 1922658
- NSF-PAR ID:
- 10218315
- Date Published:
- Journal Name:
- Advances in Neural Information Processing Systems 33 (NeurIPS 2020)
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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