Statistically unbiased prediction enables accurate denoising of voltage imaging data

Here we report SUPPORT (Statistically Unbiased Prediction utilizing sPatiOtempoRal information in imaging daTa), a self-supervised learning method for removing Poisson-Gaussian noise in voltage imaging data. SUPPORT is based on the insight that a pixel value in voltage imaging data is highly dependent on its spatially neighboring pixels in the same time frame, even when its temporally adjacent frames do not provide useful information for statistical prediction. Such spatiotemporal dependency is captured and utilized to accurately denoise voltage imaging data in which the existence of the action potential in a time frame cannot be inferred by the information in other frames. Through simulation and experiments, we show that SUPPORT enables precise denoising of voltage imaging data while preserving the underlying dynamics in the scene.

We also show that SUPPORT can be used for denoising time-lapse fluorescence microscopy images of Caenorhabditis elegans (C. elegans), in which the imaging speed is not faster than the locomotion of the worm, as well as static volumetric images of Penicillium and mouse embryos. SUPPORT is exceptionally compelling for denoising voltage imaging and time-lapse imaging data, and is even effective for denoising calcium imaging data.

For more details, please see the accompanying research publication "Statistically unbiased prediction enables accurate denoising of voltage imaging data".

Datasets for publication titled "Statistically unbiased prediction enables accurate denoising of voltage imaging data"

Voltage imaging of paQuasAr6a: paQuasAr6a.zip
paQuasAr6a/Q6a_Cell1
paQuasAr6a/Q6a_Cell2
paQuasAr6a/Q6a_Cell3
paQuasAr6a/Q6a_Cell4
paQuasAr6a/Q6a_Cell5
paQuasAr6a/Q6a_Cell6
paQuasAr6a/175118PP046_P8_pulse (10 ms)_q6
paQuasAr6a/181625PP046_P5_q6_pulse(50ms)
paQuasAr6a/183616PP046_P8_pulse (10 ms)_q6
paQuasAr6a/183717PP046_P5_q6_pulse(50ms)

Voltage imaging of Voltron2: Voltron2.zip
Voltron2/Voltron_Cell1
Voltron2/Voltron_Cell2
Voltron2/Voltron_Cell3
Voltron2/Voltron_Cell3_2
Voltron2/Voltron_Cell4
Voltron2/Voltron_Cell5
Voltron2/Voltron_Cell6
Voltron2/Voltron_Cell7 (100f_s)
Voltron2/Voltron_Cell7_2 (100 f_s)

Voltage imaging of zArchon (zebrafish spinal cord): zebrafish_spinal_cord_N.zip

Voltage imaging of SomArchon (mouse hippocampus neuron): SomArchon.zip

Volumetric structural imaging of mouse embryo (Expansion microscopy): Expansion_microscopy.zip
Expansion_microscopy/JEME208_2x_expanded_bone.tif
Expansion_microscopy/JEME208_2x_expanded_intenstine.tif
Expansion_microscopy/JEME209_2x_expanded_bone_1.tif
Expansion_microscopy/JEME209_2x_expanded_bone_2.tif
Expansion_microscopy/JEME209_2x_expanded_tail.tif

Volumetric structural imaging of penicillium: Penicillium.zip
Penicillium/penicillium_low_snr.tif
--> Low SNR image
Penicillium/penicillium_high_snr.tif
--> High SNR image

Calcium imaging of zebrafish: Zebrafish.zip
Zebrafish/zebrafish_multiple_brain_regions.tif
--> Multiple brain regions
Zebrafish/zebrafish_Cerebellar_plate.tif
--> Cerebellar plate
Zebrafish/zebrafish_Dorsal_telencephalon.tif
--> Dorsal telencephalon
Zebrafish/zebrafish_Medulla_oblongata.tif
--> Medulla oblongata
Zebrafish/zebrafish_Olfactory_bulb.tif
--> Olfactory bulb
Zebrafish/zebrafish_Optic_tectum.tif
--> Optic tectum
Zebrafish/zebrafish_Habenula.tif
--> Habenula