Extraction of 3D Point Spread Function from in-vivo Two-Photon Microscope Acquisition

Two-photon microscopy image volumes often suffer from inherent blur due to optical imperfections.
Although theoretical point spread function (PSF) estimates can be derived from optical parameters,
real-world PSFs often deviate due to misalignments or tissue-induced wavefront distortions.
We introduce a novel three-dimensional blind deconvolution approach that integrates both data-consistency and guidance terms.
 
 

General Parameters

Allowed file types: tif, tiff, nii.gz
1000

Kernel Estimation

Size per dimension: 2 - 100, pixels: 8 - 13'500
Allowed file types: tif, tiff, nii.gz

Patches for Data Fitting Term

Size per dimension: 2 - 4096, pixels: 8 - 2'097'152
 
Size per dimension: 2 - 4096, pixels: 8 - 2'097'152
Min. value per dimension: 0
 
Allowed file types: tif, tiff, nii.gz
 

Non-Blind Deconvolution Step

Please pick one of the non-blind deconvolution algorithms below:
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Output Files

After the results are ready, we will email you a link to a zip file with the following content:

├── log_deconvolution.out
├── errors_with_request.log
└── final_results
    ├── centered_max_int_final_kernel_estimate_centered.tif
    ├── final_kernel_estimate_centered_mips.png
    ├── final_kernel_estimate_centered.tif
    ├── final_kernel_estimate_mips.png
    ├── final_kernel_estimate.tif
    ├── kernel_estimate_evolution.gif
    ├── non_blind_deconv
    │   └── final_kernel_estimate_centered
    │       ├── full_volume
    │       │   └── deconwolf
    │       │       └── deconvolved_DW__.tif
    │       └── patches
    │           └── deconwolf
    │               ├── deconvolved_DW__.tif
    │               └── ...
    ├── kernel_estimate
    │   ├── step_0000
    │   │   ├── auxiliary_kernel__step_00_actual_values.tif
    │   │   ├── auxiliary_kernel__step_00_seg_mask_0.1_threshold__only_viz.tif
    │   │   ├── auxiliary_kernel__step_00_xy_xz_mip.png
    │   │   ├── auxiliary_kernel__step_00_xy_yz_mip.png
    │   │   ├── kernel_estimate__step_00_actual_values.tif
    │   │   ├── kernel_estimate__step_00_seg_mask_0.1_threshold__only_viz.tif
    │   │   ├── kernel_estimate__step_00_xy_xz_mip.png
    │   │   └── kernel_estimate__step_00_xy_yz_mip.png
    │   └── step_XXXX
    │       ├── ...
    ├── blurred_patches
    │   ├── patch_0.tif
    │   └── ...
    ├── sharp_patches
    │   ├── patch_0.tif
    │   └── ...
    ├── loss_history.csv
    ├── loss_history_HQS_1st_half.png
    ├── loss_history_HQS_2nd_half.png
    └── loss_history.png
 
 

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