Nature research paper: A transcriptomic axis predicts state modulation of cortical interneurons
After virus injection, a small bolus of red fluorescent beads , 2% solids, Thermo Fisher Scientific) was injected at the most rostral part of the craniotomy, to allow orientation of the ex vivo slices but not interfere with V1 imaging in the caudal part. After recovery, mice were habituated for handling and head‐fixation for three days before carrying out recordings.Each mouse was recorded for at least three sessions. In vivo recordings were performed 15–45 days after the virus injection.
-stack, was acquired at the same wavelength as the calcium imaging . The second one, called the referenceBefore euthanizing each mouse, we acquired structural-stacks at 1,040 nm to get an image of the mCherry cells across the whole craniotomy . This structural-stack was used to select slices on which to perform transcriptomic analysis, and to provide an initialization point for the registration algorithm.All recordings were targeted to the V1 monocular region .
Natural scenes from the ImageNet database were contrast-normalized and presented as described previously. Each image was presented for 0.5 s with an interstimulus interval uniformly distributed from 0.3 to 1.1 s. Five per cent of the total presentations was grey stimuli. During each session we presented a given set of 1,000 different natural images twice .
On each recording session we presented the same random sparse noise stimuli that were used to map retinotopy , for 30 min. Spontaneous activity was recorded in front of a uniform grey screen, set to a steady cyan level equal to the background of all the stimuli presented for visual responses protocols. The duration of these grey screen presentations was typically between 15 and 20 min.We used a collimated infrared LED to illuminate the eye contralateral to the recording site.
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