Aca2000 165 umnir

A built-in push-broom HMI system (Figure 2a) was developed, which included a microscope and hyperspectral imaging system. An Olympus Biomedical BX43 upright microscope (Olympus, Tokyo, Japan) was used in the system. A 30-W halogen lamp was utilized as the light source. The objective parameters for bright field imaging: 100×/0.90. The model number of the sensor was acA2000-165 umNIR (Basler, Ahrensburg, Germany). The spatial resolution of our hyperspectral camera was about 0.67 µm, the average spectral interval was 2.1 nm, and the field of view (FOV) was 64 × 64 μm². Then, a datacube was obtained containing 277 bands (440–1023 nm).

The self-assembled HMI system had two components. One was a hyperspectral sensor (acA2000-165 umNIR, Basler Ahrensburg, Germany) enhanced in the near-infrared wavelength range. The other was an upright microscope (BX43, Olympus, Tokyo, Japan), whose original light source was replaced by a 30 W halogen lamp to cover the wide wavelength range. In order to obtain more detailed spatial information, we used MPlanFL N (100×/0.90) as an objective lens with over 65% transmittance in the valid wavelength range. Therefore, the lens had adequate coatings to cover a wide spectral range. Owing to the advanced equipment, we obtained MDs with a wide wavelength range (440–1023 nm), a high optical resolution (0.4 um @600nm wavelength), a high spectral resolution (2.1 nm), and a large field of view (64 × 64 um²), which enabled us to detect species of infectious pathogens.

To capture whole brain neural activity in a freely behaving C.elegans, we combined a spinning disk confocal inverted microscope (Nikon Ti-U and Yokogawa CSU-W1, Japan) with a customized upright light path for worm tracking. Fluorescence signals, emitted from neurons at different depths in a head ganglion, were collected by a high NA objective (40X, NA = 0.95, Nikon Plan Apo), driven by a high-precision scanner (PI P721.CDQ). The measured lateral resolution is 0.30 μm/pixel; the scanning step along Z-axis is 1.50 μm. An imaging volume comprises 18 two-channel fluorescence images recorded at 100 fps by two sCMOS cameras (Andor Zyla 4.2, England) simultaneously. Our imaging system thus has a volume rate ≈ 5 Hz. Reducing the volume rate by increasing the inter-volume interval is not critical for CeNDeR, since both our training and inference methods are sequence-independent. A customized infrared LED ring (850 nm) was mounted above a worm, and dark-field images of worm behaviors were captured by an upright light path and recorded at 25 fps by a USB-3.0 camera (Basler acA2000–165umNIR).