Work Description

Date: 4 December 2024

Dataset Title: Behavioral modulation and molecular definition of wide-field vertical cells in the mouse superior colliculus associated dataset

Dataset Creators: X. Relota, A. Ford, E. L. Savier

Dataset Contact: Elise Savier (esavier@umich.edu)

Funding: R00EY031783 and R01EY026286 (NIH NEI)

Key Points:
• A subpopulation of neurons in the superior colliculus (NTSR1+ wide field vertical cells) display heterogenous visual responses preference and variability
• Modulation of NTSR1+ wide field vertical cells by locomotion is stimulus dependent
• NTSR1+ wide field vertical cells receive inputs from multiple brain regions
• NTSR1+ wide field vertical cells overlap with newly identified molecular markers

Research Overview:
Understanding how neuronal response preferences emerge remains a fundamental goal in neuroscience. Our ability to target neuron subpopulations and their embedding in circuits has greatly evolved over the last decades with the development of new tools from transgenic mouse lines to RNA sequencing methods. Here we focus on wide-field vertical neurons (WFV) which are found in the superior colliculus, a visual center in the midbrain that is highly conserved across species. We challenge earlier definition of this cell-type and reconcile them with more modern approaches. Due to their conservation and connectivity, WFV present a model of choice to investigate how neurons gain their response specificity and relationships between structure, function, implication in behavior and molecular profiles.

Methodology:
The data are photomicrographs of brain sections stained using viral tracing methods, fluorescent in situ hybridization and immunostaining and in vivo calcium imaging data.
Date Coverage: 2019-2024 (Date range include dates of input data to model (2018-2020), and dates of simulated outputs with various simulation types).
Instrument and/or Software specifications: MATLAB, Pschytoolbox (https://github.com/Psychtoolbox-3/Psychtoolbox-3/tree/3.0.19.14), tiff reader (Fiji recommended), Qpath.

Overview:

1) Calcium Imaging of the NTSR1-Cre mouse line in the superior colliculus in response to visual stimulus - "Calcium Imaging"
This folder contained original tif files and stimulus parameters (Original data), registered and synchronized data (Processed files) and final extracted results (Code)

2) Anatomical tracing performed using rabies tracing in the NTSR1-Cre mouse line - "Rabies tracing"
This folder contains original .n2d or .czi files in proprietary format (Original Files), universal format (Tiff files) and a snapshot of each file in .jpeg to facilitate navigation (Snapshots).

3) Fluorescent in situ hybridization in the NTSR1-Cre mouse line - "In situ hybridization"
This folder contains original in Tiff files (Tif) and a snapshot of each file in .jpeg to facilitate navigation (Snapshots)

4) Characterization of the NTSR1-Cre mouse line crossed with a reporter strain - "NTSR1-Cre x tdTomato"
This folder contains original in Tiff files (Tif) and a snapshot of each file in .jpeg to facilitate navigation (Snapshots)

5) Anatomical tracing performed using anterograde tracing in the NTSR1-Cre mouse line - "Anterograde tracing"
This folder contains original in Tiff files (Tif) and a snapshot of each file in .jpeg to facilitate navigation (Snapshots)

6) Immunofluorescence staining combined with anatomical tracings in the NTSR1-Cre mouse line - "Immunostaining"
This folder contains original in Tiff files and a snapshot of each file in .jpeg to facilitate navigation (Snapshots)

7) Quantification of immunofluorescence staining - "IF Quantification"
This folder contains projected photomicrograph including masks (ROI.zip) and associated snapshots (Quantification)

8) Quantification of in situ hybridization staining - "ISH Quantification"
This folder contains projected photomicrograph including masks (ROI.zip) and associated snapshots (Quantification).

1) Files associated with "Calcium imaging"

Results from 5 animals, named on the following nomenclature:
Original_Mouse_AnimalID_Data, containing each 5 TSeries,corresponding to the 5 types of stimuli used and a metadata.xml describing how files are associated with each other. These files are compressed with 7zip.

Original_Mouse_WS_B_10132022 - metadata.xml and associated stimulus files generated by Psychstim
Recording1
TSeries-10132022-1221_WS_B_DG-617 - tiff files and associated metadata
TSeries-10132022-1221_WS_B_FS-618 - tiff files and associated metadata
TSeries-10132022-1221_WS_B_Loom-615 - tiff files and associated metadata
TSeries-10132022-1221_WS_B_MD-616 - tiff files and associated metadata
TSeries-10132022-1221_WS_B_MS-614 - tiff files and associated metadata

Original_Mouse_WS_H_11062022- metadata.xml and associated stimulus files generated by Psychstim
Recording1
TSeries-11062022-0745_WSH_MS_z362-643- tiff files and associated metadata
TSeries-11062022-0859_WSH_DG_z362-648- tiff files and associated metadata
TSeries-11062022-0859_WSH_FS_z362-649- tiff files and associated metadata
TSeries-11062022-0859_WSH_Loom_z362-646- tiff files and associated metadata
TSeries-11062022-0859_WSH_MD_z362-647- tiff files and associated metadata

Original_Mouse_WS_G_11032022
Recording1
TSeries-11032022-0921_WSG_DG-636- tiff files and associated metadata
TSeries-11032022-0921_WSG_FS-637- tiff files and associated metadata
TSeries-11032022-0921_WSG_Loom-634- tiff files and associated metadata
TSeries-11032022-0921_WSG_MD-635- tiff files and associated metadata
TSeries-11032022-0921_WSG_MS-633- tiff files and associated metadata

Original_Mouse_VDWFS_R_12312021
Recording1
TSeries-12312021-0900_VDWFS_R_DG-7533- tiff files and associated metadata
TSeries-12312021-0900_VDWFS_R_Loom-7536- tiff files and associated metadata
TSeries-12312021-0900_VDWFS_R_MD-7534- tiff files and associated metadata
TSeries-12312021-0900_VDWFS_R_MS-7535- tiff files and associated metadata
TSeries-12312021-0900_VDWFS_R_RFmapping-7532- tiff files and associated metadata

Original_Mouse_WS_K_11042022
Recording1
TSeries-11042022-0738_WSK_z387_DG_1_5x-641- tiff files and associated metadata
TSeries-11042022-0738_WSK_z387_FS_1_5x-642- tiff files and associated metadata
TSeries-11042022-0738_WSK_z387_Loom_1_5x-639- tiff files and associated metadata
TSeries-11042022-0738_WSK_z387_MD_1_5x-640- tiff files and associated metadata
TSeries-11042022-0738_WSK_z387_MS_1_5x-638- tiff files and associated metadata

DG: Drifting gratings, FS: Flashing Spot, Loom: Looming, MD: Moving Dots, MS: Moving Spot

Each of animal has a corresponding "Processed__Mouse_AnimalID_Data" folder which contains the following files, which can be read in Matlab.
Code used to generate these files is available upon request to Hui Chen (hc6cb@virginia.edu) and Jianhua Cang (cang@virginia.edu) at the University of Virginia.

averageImage.mat
averageTraces.mat
DG_40deg.mat or Looming4speeds.mat or MovingDotsWF.mat or Onespot4dir.mat or SlowFlashWF.mat, depending on the stimulus
ImageFileNames.mat
Parameters_DeltaFbyFo.mat
recordingCharacteristics.mat
ReferenceChannel.mat
relativeTime.mat
ResponsesChannel.mat
ROI_Data.mat
ROI_Data_Raw.mat
ROI_Data_Running.mat
ROIs.mat
running.mat
StimulusChannel.mat
stimulusData.mat
voltageConditionNumbers.dat
vxml.mat
xml.mat
yxShift.mat

2) Files contained in "Rabies Tracing Tif" and "Rabies Tracing Snapshot", .tif and .jpg respectively
Details for each photomicrograph can be found in WFVDatasetfilelistRabiesTracing.pdf

NTSR1_mCherryRetro_8_Retina_Top_quadrant_20x_2021
NTSR1_mCherryRetro_8_SC_10x_TileswDAPI
NTSR1_mCherryRetro_8_V1_10x
NTSR1_mCherryRetro_8_V1_10x_0.5
NTSR1_mCherryRetro_10_Starters_20x
NTSR1_mCherryRetro_10_Starters_deeper_20x
NTSR1_mCherryRetro_10_V1V2_20x
NTSR1_mCherryRetro7_PBG_5x
NTSR1_mCherryRetro7_PBG_20x
NTSR1_mCherryRetro7_PBG_20xtiles
NTSR1_mCherryRetro7_pretectum20x
NTSR1_mCherryRetro7_pretectumandvLGN_5x
NTSR1_mCherryRetro7_Retina_10x
NTSR1_mCherryRetro7_Retina_20x
NTSR1_mCherryRetro7_SCstarters_20x
NTSR1_mCherryRetro7_V15x
NTSR1_mCherryRetro7_V110x
NTSR1_mCherryRetro7_V220x
NTSR1_mCherryRetro7_vLGN20x
NTSR1_retro7_mCherry_SC40x
NTSR1Cre_Retro4_GFP_Retina_5x
NTSR1Cre_Retro4_GFP_Retina_20x
NTSR1Cre_Retro4_GFP_V1_20x
NTSR1_mCherryRetro_8_Retina_5x_2021
NTSR1_mCherryRetro_8_Retina_10x
NTSR1_mCherryRetro_8_Retina_10x_dapi
NTSR1_mCherryRetro_8_Retina_bottom_quadrant_20x_2021
NTSR1_mCherryRetro_8_Retina_left_quadrant_20x_2021
NTSR1_mCherryRetro_8_Retina_right_quadrant_20x_2021

PBG: Parabigeminal nucleus, vLGN: ventral Lateral Geniculate Nucleus, V1: Primary Visual Cortex

3) Files contained in "In Situ Hybridization Tif" and "In Situ Hybridization Snapshot", .tif format and .jpg, respectively
Details for each photomicrograph can be found in WFVDatasetfilelistInSituHybridization.pdf

CNN1_CBLN520_NPNT570_NECAB650_leftSC_Section1_medial_40x
CNN1_CBLN520_NPNT570_NECAB650_leftSC_Section2_lateral_40x
CNN1_CBLN520_NPNT570_NECAB650_rightSC_Section1_lateral_40x
CNN1_CBLN520_NPNT570_NECAB650_rightSC_Section1_medial_40x
CNN3_CBLN520_NPNT570_NECAB650_leftSC_Section1_lateral_40x
CNN3_CBLN520_NPNT570_NECAB650_leftSC_Section1_medial_40x
CNN3_CBLN520_NPNT570_NECAB650_leftSC_Section2_lateral_40x
CNN3_CBLN520_NPNT570_NECAB650_leftSC_Section2_medial_40x
CNN4_CBLN520_NPNT570_NECAB650_leftSC_Section1_lateral_40x
CNN4_CBLN520_NPNT570_NECAB650_leftSC_Section1_medial_40x
CNN4_CBLN520_NPNT570_NECAB650_rightSC_Section1_medial_40x
CNN4_CBLN520_NPNT570_NECAB650_rightSC_Section2_lateral_40x
CTN1_CBLN520_TDTOM570_NECAB650_leftSC_Section1_lateral_40x
CTN1_CBLN520_TDTOM570_NECAB650_leftSC_Section2_medial_40x
CTN1_CBLN520_TDTOM570_NECAB650_rightSC_Section2_medial_40x
CTN2_CBLN520_TDTOM570_NECAB650_leftSC_Section1_medial_40x
CTN2_CBLN520_TDTOM570_NECAB650_leftSC_Section2_medial_40x
CTN2_CBLN520_TDTOM570_NECAB650_rightSC_Section1_lateral_40x
CTN2_CBLN520_TDTOM570_NECAB650_rightSC_Section2_lateral_40x
CTN3_CBLN520_TDTOM570_NECAB650_leftSC_Section1_medial_40x
CTN3_CBLN520_TDTOM570_NECAB650_rightSC_Section1_lateral_40x
CTN3_CBLN520_TDTOM570_NECAB650_rightSC_Section1_medial_40x
CTN3_CBLN520_TDTOM570_NECAB650_rightSC_Section2_lateral_40x
NT1_NPNT520_tdTom570_entireSC_20x tile

4) Files contained in "NTSR1-Cre x tdTomato Tif" and "NTSR1-Cre x tdTomato Snapshot", .tif format and .jpg, respectively
Details for each photomicrograph can be found in WFVDatasetfilelistNTSR1-CrextdTomato.pdf

NTSR1xAi14_EntireSection_sagittal_10x
NTSR1xAi14_Retina_Cryosection_40x
NTSR1xAi14_Retina_Flatmount_10x
NTSR1xAi14_SC_Flx_GFP_40x
NTSR1xAi14_SC_Flx_GFP_40x_Section2
NTSRxAi9_AnteroV1_Sparse_GFP_SC10x
NTSRxAi9_AnteroV1_Sparse_GFP_SC20x

5) Files contained in "Anterograde Tracing Tif" and "Anterograde Tracing Snapshot", .tif format and .jpg, respectively
Details for each photomicrograph can be found in WFVDatasetfilelistAntrogradeTracing.pdf

U1_NTSR1Cre_Flx_G6f_SC_injectionSC_D1C6_20x
U1_NTSR1Cre_Flx_G6f_SC_LP_projection_10x
WFiiiE_NTSR1Cre_Flx_G6f_SC_injectionSC_D2C6_10x
WFiiiE_NTSR1Cre_Flx_G6f_SC_projectionLP_D7C1_10x
WFiiiF_NTSR1Cre_Flx_G6f_5_LP_5x_2021
WFiiiF_NTSR1Cre_Flx_G6f_pretectum_2_5x_2021
WFiiiF_NTSR1Cre_Flx_G6f_pretectum_4_LP_5x_2021
WFiiiF_NTSR1Cre_Flx_G6f_SC_5x_2021
WFiiiF_NTSR1Cre_Flx_G6f_SC_injectionSC_D1C5_10x
WFiiiF_NTSR1Cre_Flx_G6f_SC_projection_D4C7_5x
WFiiiF_NTSR1Cre_Flx_G6f_SC_projection_D4C7_10x
WFiiiF_NTSR1Cre_Flx_G6f_SC_projectionLP_5x
WFiiiF_NTSR1Cre_Flx_G6f_SC_projectionLP_10x
WFiiiF_NTSR1Cre_Flx_G6f_SC_projectionPBG_10x2

6) Files contained in "Immunostaining Tif" and "Immunostaining Snapshot", .tif format and .jpg, respectively
Details for each photomicrograph can be found in WFVDatasetfilelistImmunostaining.pdf

WFA11_NTSR1_SC_flx_tdTom_PBG_vglut488_tdt_synphy647_60x zstack
WFA11_NTSR1_SC_flx_tdTom_Pul_vglut488_tdt_synphy647_60x zstack
WFA12_NTSR1_SC_flx_tdTom_PBG_vglut488_tdt_synphy647_60x zstack
WFA12_NTSR1_SC_flx_tdTom_Pul_vglut488_tdt_synphy647_60x zstack
WFA13_NTSR1_SC_flx_tdTom_PBG_vglut488_tdt_synphy647_60x zstack
WFA13_NTSR1_SC_flx_tdTom_Pul_vglut488_tdt_synphy647_60x zstack
WFA14_NTSR1_SC_flx_tdTom_PBG_vglut488_tdt_synphy647_60x zstack
WFA14_NTSR1_SC_flx_tdTom_Pul_vglut488_tdt_synphy647_60x zstack

7) Files contained in each folder within "Immunostaining quantification" - Animal 11 to 14, same files can be found within each animal folder

11pbgRoiSet.zip - ROI mask to be read using FIJI, delineates the boundary of the region of interest quantified
11pulvRoiSet.zip - ROI mask to be read using FIJI, delineates the boundary of the region of interest quantified
PBG_60x zstack.tif - Original photomicrograph in universal format
PBG_vglut488_tdt_synphy647_60x zstack.nd2 - - Original photomicrograph in proprietary format
pulv_60x zstack.tif - - Original photomicrograph in universal format
pulv_vglut488_tdt_synphy647_60x zstack.nd2 - Original photomicrograph in proprietary format
TRIM_PBG_60x zstack-1.tif - Adjusted photomicrograph in universal format
TRIMpulv_60x zstack-1.tif - Adjusted photomicrograph in universal format

8) Files contained in each folder within "In situ hybridization quantification" - Animal CNN1, CNN3, CNN4, CTN1, CTN2, CTN3, same files can be found within each animal folder

CellCounter_MAX_CNN1_leftSC_Section1_medial_40x.xml - Classification result to be read using FIJI
CellCounter_MAX_CNN1_leftSC_Section2_lateral_40x.xml -Classification result to be read using FIJI
CellCounter_MAX_CNN1_rightSC_Section1_lateral_40x.xml - Classification result to be read using FIJI
CellCounter_MAX_CNN1_rightSC_Section1_medial_40x.xml - Classification result to be read using FIJI
CNN1left1MedRoiSet.zip - ROI mask to be read using FIJI, delineates the boundary of the region of interest quantified
CNN1left2LatRoiSet.zip - ROI mask to be read using FIJI, delineates the boundary of the region of interest quantified
CNN1right1LatRoiSet.zip - ROI mask to be read using FIJI, delineates the boundary of the region of interest quantified
CNN1right1medRoiSet.zip - ROI mask to be read using FIJI, delineates the boundary of the region of interest quantified
MAX_CNN1_leftSC_Section1_medial_40x.tif - Projected photomicrograph in universal format
MAX_CNN1_leftSC_Section2_lateral_40x.tif - Projected photomicrograph in universal format
MAX_CNN1_rightSC_Section1_lateral_40x.tif - Projected photomicrograph in universal format
MAX_CNN1_rightSC_Section1_medial_40x.tif - Projected photomicrograph in universal format

Related publication(s):
Relota, X., et al. (2024). Behavioral modulation and molecular definition of wide-field vertical cells in the mouse superior colliculus. Forthcoming.

Use and Access:
This data set is made available under a Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0).

To Cite Data:
Savier Elise L. Behavioral modulation and molecular definition of wide-field vertical cells in the mouse superior colliculus associated dataset [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/mja2-ra07