Data from: Stable excitatory-inhibitory synapse balance despite dynamic turnover
Data files
Jul 28, 2026 version files 19.24 GB
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DIV11_405-BFP_488-mClover-Homer1_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy3_analysismask01.roi
316 B
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DIV11_405-BFP_488-mClover-Homer1_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy3_analysismask02.roi
316 B
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DIV11_405-BFP_488-mClover-Homer1_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy3.ome.tif
1.83 GB
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DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask01.roi
272 B
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DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask02.roi
272 B
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DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask03.roi
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DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
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DIV13_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask01.roi
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DIV13_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask02.roi
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DIV13_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
2.18 GB
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DIV14_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy6_analysismask01.roi
278 B
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DIV14_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy6_analysismask02.roi
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DIV14_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy6.ome.tif
1.87 GB
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DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy1_analysismask.roi
284 B
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DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy1.ome.tif
1.84 GB
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DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5_analysismask.roi
284 B
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DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5.ome.tif
1.88 GB
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DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy5_analysismask01.roi
270 B
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DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy5_analysismask02.roi
270 B
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DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy5.ome.tif
2.18 GB
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DIV8_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy7_analysismask01.roi
276 B
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DIV8_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy7_analysismask02.roi
276 B
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DIV8_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy7.ome.tif
1.75 GB
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DIV9_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy4_analysismask01.roi
270 B
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DIV9_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy4_analysismask02.roi
270 B
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DIV9_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy4.ome.tif
2.14 GB
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DIV9_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5_analysismask.roi
272 B
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DIV9_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5.ome.tif
1.75 GB
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README.md
7.56 KB
Abstract
Functional balance between excitatory and inhibitory synapses is critical for neural circuit behavior. How this balance is established and maintained during development is poorly understood. To address this, we concurrently imaged fluorescently-tagged pre- and post-synaptic compartments in primary hippocampal neuronal cultures over relative long time periods (15 hours). We observed continual turnover of subsets of excitatory and inhibitory synaptic structures, yet densities of excitatory and inhibitory synapses remained stable through development.
Dataset DOI: 10.5061/dryad.5qfttdzp5
Description of the data and file structure
This repository is related to the following publication: Garbett, Allen et al. Stable excitatory-inhibitory synapse balance despite dynamic turnover. eLife, 2026
Files included are ome.tif of Denoised (NIS-Elements) and Extended Depth of Focus (NIS-Elements) projected images (original data are three z-steps of 0.5 µm step size). All images are single z-step, 4-channel, time-series with 181 time points, with 5 min interval between each timepoint. Metadata from original acquisition is included in the ome.tifs for further information on laser powers and acquisition settings.
File names indicate the condition and tif channel identity. For an example the file:
DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy5.ome.tif
Is from neuronal cultures at 8 Days In Vitro (DIV), expressing BFP (mTagBFP2) imaged with 405 excitation laser, mClover-Homer1 imaged with 488 excitation, and HaloTag-Syb2 with 640 excitation.
Also included are *_analysismask.roi files which are Imagej/FIJI region of interest files that can be used to determine the crop areas used for subsequent analysis in the related manuscript.
For code used for the analysis of this manuscript, please see the github repository at:
https://github.com/datajamesallen/Garbett_2026_eLife
For further information on the methodology of this study please see the related manuscript.
Files and variables
File: DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy5_analysismask01.roi
Description: Analysis region 1 for DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy5.ome.tif
File: DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy5_analysismask02.roi
Description: Analysis region 2 for DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy.ome.tif
File: DIV8_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy7_analysismask01.roi
Description: Analysis region 1 for DIV8_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy7.ome.tif
File: DIV8_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy7_analysismask02.roi
Description: Analysis region 2 for DIV8_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2
File: DIV9_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy4_analysismask01.roi
Description: Analysis region 1 for DIV9_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy4.ome.tif
File: DIV9_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy4_analysismask02.roi
Description: Analysis region 2 for DIV9_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy4.ome.tif
File: DIV9_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5_analysismask.roi
Description: Analysis region 1 for DIV9_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5.ome.tif
File: DIV11_405-BFP_488-mClover-Homer1_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy3_analysismask01.roi
Description: Analysis region 1 for DIV11_405-BFP_488-mClover-Homer1_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy3.ome.tif
File: DIV11_405-BFP_488-mClover-Homer1_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy3_analysismask02.roi
Description: Analysis region 2 for DIV11_405-BFP_488-mClover-Homer1_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy3.ome.tif
File: DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask01.roi
Description: Analysis region 1 for DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
File: DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask02.roi
Description: Analysis region 2 for DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
File: DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask03.roi
Description: Analysis region 3 for DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
File: DIV13_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask01.roi
Description: Analysis region 1 for DIV13_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
File: DIV13_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2_analysismask02.roi
Description: Analysis region 2 for DIV13_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
File: DIV14_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy6_analysismask01.roi
Description: Analysis region 1 for DIV14_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy6.ome.tif
File: DIV14_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy6_analysismask02.roi
Description: Analysis region 2 for DIV14_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy6.ome.tif
File: DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy1_analysismask.roi
Description: Analysis region 1 for DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy1.ome.tif
File: DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5_analysismask.roi
Description: Analysis region 1 for DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5.ome.tif
File: DIV8_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy5.ome.tif
Description: Neuronal cultures 8 Days in Vitro expressing mTagBFP2, mClover-Homer1, and HaloTag-Syb2
File: DIV8_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy7.ome.tif
Description: Neuronal cultures 8 Days in Vitro expressing mTagBFP2, tdTomato-Gephyrin, and HaloTag-Syb2
File: DIV9_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy4.ome.tif
Description: Neuronal cultures 9 Days in Vitro expressing mTagBFP2, mClover-Homer1, and HaloTag-Syb2
File: DIV9_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5.ome.tif
Description: Neuronal cultures 9 Days in Vitro expressing mTagBFP2, tdTomato-Gephyrin, and HaloTag-Syb2
File: DIV11_405-BFP_488-mClover-Homer1_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy3.ome.tif
Description: Neuronal cultures 11 Days in Vitro expressing mTagBFP2, mClover-Homer1, tdTomato-Gephyrin, and HaloTag-Syb2
File: DIV11_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
Description: Neuronal cultures 11 Days in Vitro expressing mTagBFP2, mClover-Homer1, and HaloTag-Syb2
File: DIV13_405-BFP_488-mClover-Homer1_640-HaloTag-Syb2_xy2.ome.tif
Description: Neuronal cultures 13 Days in Vitro expressing mTagBFP2, mClover-Homer1, and HaloTag-Syb2
File: DIV14_405-BFP_561-tdTomato-Gephyrin_640-HaloTag-Syb2_xy6.ome.tif
Description: Neuronal cultures 14 Days in Vitro expressing mTagBFP2, tdTomato-Gephyrin, and HaloTag-Syb2
File: DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy1.ome.tif
Description: Neuronal cultures 14 Days in Vitro expressing mTagBFP2, endogenously tagged tdTomato-Gephyrin, and HaloTag-Syb2
File: DIV14_405-BFP_561-TKIT-tdTomato-Gephyrin_640-HaloTag-Syb2_xy5.ome.tif
Description: Neuronal cultures 14 Days in Vitro expressing mTagBFP2, endogenously tagged tdTomato-Gephyrin, and HaloTag-Syb2
Code/software
Code to run end-to-end analysis of the provided data can be found here:
https://github.com/datajamesallen/Garbett_2026_eLife
The github repository includes code to correct for microscope stage drift related motion, segment, and track synapses, as well as additional script to summarize and compile results. Detailed information on how to run and use the code can be found on the github repository.
