Figure 2.
- ID
- ZDB-FIG-230213-8
- Publication
- Thomson et al., 2022 - Gigapixel imaging with a novel multi-camera array microscope
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(A) Example frame of stitched gigapixel video of 130 wildtype zebrafish, 8 days old (similar imaging experiment repeated 11 times). An object detection pipeline (Faster-RCNN) is used to detect and draw bounding boxes around each organism. Bounding boxes include detection confidence score (for more details see Methods). Each bounding box’ image coordinates is saved and displayed on stitched full frame image. Zoom in shows three individual fish (blue box). Scale bar: 1 cm. (B) Headshots of nine zebrafish whose images used to train a siamese neural network (see Methods, Appendix 1—figure 6). Colors indicate the fish identity used to visualize performance in (C). Each fish has a distinct melanophore pattern, which are visible due to the high resolution of MCAM. Scale bar: 1 mm. (C) Two-dimensional t-SNE visualization of the 64-dimensional image embeddings output from the siamese neural network, showing that the network can differentiate individual zebrafish. For 9 zebrafish, 9 clusters are apparent, with each cluster exclusively comprising images of one of the 9 fish (each dot is color-coded based on ground truth fish identity), suggesting the network is capable of consistently distinguishing larval zebrafish (62 training epochs, 250 augmented images per fish). (D) Close-up of three zebrafish with tail tracking; original head orientation shown in gray (bottom right). (E) Automated eye tracking from cropped zebrafish (see Methods for details); results histogram of eye angles measured on 93 zebrafish across 20 frames. (F) Optical schematic of stereoscopic depth tracking. The depth tracking algorithm first uses features to match an object between cameras (top) and then calculates the binocular disparity between the two cameras to estimate axial position with an approximate resolution of 100 µm along z (verified in calibration experiments at 50 axial positions). (G) Example 3D trajectories for 3 zebrafish from recorded gigapixel video of 93 individuals, with z displacement estimated by stereoscopic depth tracking.
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