Published May 8, 2023 | Version 1
Dataset Open

Confocal and STED Live F-actin dataset

  • 1. Université Laval

Contributors

  • 1. Université Laval

Description

Paired confocal and STED images of F-actin nanostructures in living neurons using the far-red fluorogenic dye SiR-Actin. This dataset was used to train and test the TA-GAN model for confocal-to-STED super-resolution of axonal and dendritic F-actin in living neurons (Resolution Enhancement with a Task-Assisted GAN to Guide Optical Nanoscopy Image Analysis and Acquisition).

All images : 20 nm/pixel.

Folders:
- train : 753 pairs of confocal/STED images (varying sizes)
- valid : 47 pairs of confocal/STED images (varying sizes)
- test_initial & test_final : 84 confocal/STED pairs acquired before (initial) and 84 acquired after (final) control sequences where 15 confocal images of the full FOV (500 x 500 pixels = 10μm x 10μm) were acquired at 1 frame/minute. In addition to the confocal image, a sub-region (100 x 100 pixels = 2μm x 2μm) was selected outside the central ROI (300 x 300 pixels = 6μm x 6μm) and acquired with the STED modality at every time step; the signal decrease due to photobleaching effects can therefore be more prononced in the border region outside the central ROI.
- test_series : contains 149 series of images acquired with TA-GAN assistance using the change-based Dice coefficient threshold or the variability-based threshold. 

The test_series folder contains folders with names corresponding to "[date of acquisition]_cs[coverslip number]_ROI[selected region number]". Each folder contains three subfolders : input, full_STED, and initial_final_confocal. 
- Input : this folder contains three-channel images for each of the 15 frames in the series. The first channel is the full FOV confocal image (10μm x 10μm), the second channel is the STED sub-region (2μm x 2μm) with zero-padding to match the shape of the FOV, and the third channel is a decision map of 0s and 1s, with the 1s indicating the position in the FOV of the STED sub-region.
- full_STED : this folder contains all the STED FOVs (10μm x 10μm) acquired when triggered by the TA-GAN assistance. The number of full_STED FOVs varies from 0 to 15 per region, with a mean of 2.8 STED images per series. The full FOV STED images acquired before (initialSTED.tif) and after (finalSTED.tif) the series of 15 frames are also included.
- initial_final_confocal : The full FOV confocal images acquired before (initialConfocal.tif) and after (finalConfocal.tif) the series of 15 frames.

Files

LiveFActinDataset.zip

Files (742.3 MB)

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Additional details

References

  • Bouchard, C., Wiesner, T., Deschênes, A., Bilodeau, A., Gagné, C., & Lavoie-Cardinal, F. (2021). Resolution Enhancement with a Task-Assisted GAN to Guide Optical Nanoscopy Image Analysis and Acquisition. bioRxiv, 2021-07.