MiXCR: software for comprehensive adaptive immunity profiling

DA Bolotin, S Poslavsky, I Mitrophanov, M Shugay… - Nature …, 2015 - nature.com
DA Bolotin, S Poslavsky, I Mitrophanov, M Shugay, IZ Mamedov, EV Putintseva
Nature methods, 2015nature.com
fy this observation, we extracted the maximum of the post-stimulus signal in the five most
responsive regions in both experiments. In 2P imaging, all regions displayed a substantial
response at the lowest stimulus intensity, which rapidly reached a plateau as the visual
stimulation became more intense (Supplementary Figs. 5 and 6, and Fig. 1c). During 1P
imaging, the visually evoked activity was mostly confined to the tectal neuropil, the region
that receives direct projections from retinal ganglion cells. To elicit measurable signals in …
fy this observation, we extracted the maximum of the post-stimulus signal in the five most responsive regions in both experiments. In 2P imaging, all regions displayed a substantial response at the lowest stimulus intensity, which rapidly reached a plateau as the visual stimulation became more intense (Supplementary Figs. 5 and 6, and Fig. 1c). During 1P imaging, the visually evoked activity was mostly confined to the tectal neuropil, the region that receives direct projections from retinal ganglion cells. To elicit measurable signals in other brain areas, the stimulus intensity had to be increased up to 4,500 µW cm–2, beyond physiologically relevant levels. The exact mechanism by which 1P illumination leads to the observed reduction in visual sensitivity remains to be elucidated. The photoreceptors in the retina may receive excitation light scattered by the observation chamber or by the brain tissue, increasing the response threshold to subsequent visual stimuli. Alternatively, the visually evoked neural response may be attenuated owing to direct activation of light-sensitive cells throughout the brain. In any case, our results highlight the potential problems associated with visible illumination wavelengths and argue for the use of near-infrared wavelengths when studying visually driven processes. 2P light-sheet imaging combines the advantages of near-infrared illumination with the high speed of light-sheet microscopy. We produced 3D maps of flash-responsive neurons in a single experiment by sequentially moving the recorded plane across the brain and simultaneously recorded> 36,000 individual neurons at 1 Hz
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