DOI: 10.5061/dryad.w9ghx3fv1
title: An entorhinal-like region in food-caching birds

description: The mammalian entorhinal cortex routes inputs from diverse sources into
 the hippocampus. This information is mixed and expressed in the activity
 of many specialized entorhinal cell types, which are considered
 indispensable for hippocampal function. However, functionally similar
 hippocampi exist even in non-mammals that lack an obvious entorhinal
 cortex, or generally any layered cortex. To address this dilemma, we
 mapped extrinsic hippocampal connections in chickadees, whose hippocampi
 are used for remembering numerous food caches. We found a well-delineated
 structure in these birds that is topologically similar to the entorhinal
 cortex and interfaces between the hippocampus and other pallial regions.
 Recordings of this structure revealed entorhinal-like activity, including
 border and multi-field grid-like cells. These cells were localized to the
 subregion predicted by anatomical mapping to match the dorsomedial
 entorhinal cortex. Our findings uncover an anatomical and physiological
 equivalence of vastly different brains, suggesting a fundamental nature of
 entorhinal-like computations for hippocampal function.
description: # An entorhinal-like region in food-caching birds
 [https://doi.org/10.5061/dryad.w9ghx3fv1](https://doi.org/10.5061/dryad.w9ghx3fv1) ## Description of the data and file structure anatomy.mat: a 1x15 data containing all anatomical data. Data for each bird is found in a separate row of the structure. This structure has 2 fields * bird: the birdID for the animal * data: a nx8 table. n is the number of detected retrogradely labelled cells in the pallium. For each cell, the following information is stored: * ROI: the region of interest where the cell was located. This could be 'DL/CDL','HD','NFL','NIL\_M' or 'NIL\_L'. * Long: the long axis coordinate of the injection. Is either -1, 1, 3, or 5 (see Supplemental table 1) * Transverse: the transverse coordinate of the injection. Is either 'Hp' or 'DL' * Hemisphere: the hemisphere of the injection. Is either 'R' or 'L' for right or left hemisphere respectively. * AP: The AP coordinate of the cell relative to lambda in mm. Note that coronal sections were made in 0.1 mm incriments * ML: The ML coordinate of the cell relative to the midline in mm. Note that positive values here indicates the direction in the ipsilateral hemisphere * DV: the DV coordinate of the cell in sterotaxic coordinates (see Methods). Note that positive values here are more dorsal and negative are more ventral. * wavelength: the fluorophore of CTB used in the injection. Is either '488','555', or '647' physiology.mat: A 4x3 data structure organized by bird and by condition. Each column corresponds to a different recording location: * column 1: anterior DL * column 2: posterior DL * column 3: anterior hippocampus Each row corresponds to a different bird. Data for each bird is contained in a separate structure with the following fields: * birdID: band identifier for that bird * recordingLocation: aDL, pDL, or aHp * Behavior: a structure containing for each session the raw behavioral data. This structure has 4 fields: * date: the date in yyyymmdd format on which the recording session took place. * xpos: a 1xn vector of the x-position of the bird's head in mm for each recorded frame of the calcium imaging. n is the number of imaging frames. * ypos: a 1xn vector of the y-position of the bird's head in mm. * headAngle: a 1xn vector of the bird's head angle in radians relative to the wall with the door. * Calcium: a structure containing for each session the extracted calcium imaging data. This structure has 2 fields: * date: the date in yyyymmdd format on which the recording session took place. * S: a mxn matrix of the extracted calcium signal for each session. m is the number of extracted units and n is the number of calcium imaging frames. This is the output of CNMF\_E. * Tuning: a structure containing all of the tuning curves for each extracted unit in each session. This structure has 7 fields. For all fields, m is the number of extracted units: * date: the date in yyyymmdd format on which the recording session took place. * spatialMap: a mx40x40 matrix of the smoothed spatial firing maps for each unit. * fieldSegmentation: a mx40x40 matrix of the assigned fields for each spatial map. Here, 0 is a spatial location out of the fields, and integers 1:f are the pixels corresponding to fields 1:f; * temporalShift: a mx81 matrix of the skaggs spatial information values corresponding to neural activity of each unit shifted t frames relative to behavior. Each row contains data for a separate unit. This corresponds to a -40:40 frame shift, or a -2:2 second shift. * headDirectionTuning: a mx40 matrix of the smoothed head direction firing for each unit in evt/s. Firing is shown averaged to 0:pi/20:2pi-pi/20 radians for each bin. * speedTuning: a mx40 matrix of the smoothed average speed tuning of each unit in evt/s. For each row, average firing is calculated relative to the animal's speed at 0:0.5:20 cm/s * dashTuning: a mx201 matrix of the smoothed average speed tuning of each unit in evt/s. For each row, firing is shown relative to -100:100 frames relative to the start of the dash, or -5:5 seconds * Parameter: a structure containing all of the parameters for each extracted unit in each session. This structure has 15 fields. For all fields, m is the number of extracted units: * date: the date in yyyymmdd format on which the recording session took place. * normSpatialInfo: a mx1 vector containing the normalized spatial information for each recorded unit. * pSpatial: a mx1 vector containing the p-value for spatial information relative to circularly permuted data. * stability: a mx1 vector containing the average pearson correlation value for spatial maps calculated on half of the behavioral session for the other half. * pStability: a mx1 vector containing the p-value for stability relative to circularly permuted data. * borderScore: a mx1 vector containing the border score for each unit. * pBorder: a mx1 vector containing the p-value for the border score relative to circularly permuted data. * headDirectionScore: a mx1 vector containing the mean vector length for each head direction tuning curve. * pHeadDirection: a mx1 vector containing the p-value for the MVL relative to circularly permuted data. * speedScore: a mx1 vector containing the speed score (see methods) for each unit. * pSpeed: a mx1 vector containing the p-value for the speed score relative to circularly permuted data. * dashScore: a mx1 vector containing the dash score (see methods) for each unit. * pDash: a mx1 vector containing the p-value of the dash score relative to circularly permuted data. * modelFeatures: a mx4 table indicating for each of the m units which components of the model improved the fit over chance. Components that were considered were spatial location, head direction, speed, and time relative to dash. 1 indicates an improvement, 0 is no improvement. See methods and figure 7. * bestFitModel: a mx4 table indicating for each of the m units whether the best-fit model contained each component. 1 indicates an improvement, 0 is no improvement.