DOI: 10.5281/zenodo.18686251
title: Aydin Example Datasets: Microscopy and Natural Images for Image Denoising Benchmarks

description: A curated collection of 29 example images used by
Aydin, a self-supervised image
denoising toolkit for n-dimensional microscopy and natural images. These datasets
serve as benchmarks for testing and demonstrating Aydin's classical, feature-based,
and deep-learning denoising algorithms.


The collection spans 2D natural images, noisy test images, 3D fluorescence
microscopy volumes, 2D+t and 3D+t time-lapse sequences from light-sheet,
spinning-disk confocal, and widefield fluorescence microscopy.





How to use these files


Individual file access (no authentication required):
GET https://zenodo.org/api/records/{record_id}/files/{filename}/content


From Python (with Aydin installed):
from aydin.io.datasets import newyork; image = newyork()


Large TIFF files have been losslessly compressed using TIFF zstd
compression with horizontal differencing predictor. They can be read directly by
tifffile,
ImageJ/FIJI,
and most modern TIFF readers without any decompression step.





File inventory


2D Natural Images (monochrome, uint8)



newyork.png — 1024×1024, 0.7 MB.
    Original photograph of New York City by Loic A. Royer.
    CC BY 4.0.


scafoldings.png — 1024×1536, 1.0 MB.
    Original photograph of scaffoldings by Loic A. Royer.
    CC BY 4.0.


andromeda.png — 1024×1024, 0.5 MB.
    Isaac Roberts, 1888 long-exposure photograph of M31 (Andromeda Galaxy),
    taken with a 20-inch reflecting telescope at Maghull, Liverpool.
    Public domain (copyright expired; photographer died 1904).
    Wikipedia |
    Science Museum Group


pollen.png — 600×788, 0.3 MB.
    Scanning electron micrograph of pollen grains by Louisa Howard & Charles Daghlian,
    Dartmouth Electron Microscope Facility.
    Public domain (released by Dartmouth College).
    Source


characters.jpg — 1355×875, 0.3 MB.
    Comparative chart of ancient writing systems (Cuneiform, Egyptian hieroglyphs, Chinese).
    Public domain (Wikimedia Commons).


periodic_noise.png — 473×1024, 0.4 MB.
    Newspaper scan with moiré noise, from OpenCV documentation.
    Apache 2.0 / BSD-3.
    Tutorial



2D Noisy Images



fountain.png — 588×402, uint8+alpha, 0.3 MB.
    Wallace fountain from the University of Edinburgh image processing test library.
    Public domain / open access.


monalisa.png — 568×382, uint8+alpha, 0.2 MB.
    Leonardo da Vinci — Mona Lisa (c. 1503) with synthetic noise.
    Public domain.
    Wikipedia


Gauss_noisy.png — 1305×1024, uint8 RGB, 3.2 MB.
    Portrait of Carl Friedrich Gauss by C.A. Jensen (1840) with synthetic noise.
    Public domain (artist died 1870).
    Wikipedia


newyork_noisy.tif — 1024×1024, float32, 3.1 MB.
    Derived from newyork.png with synthetic Poisson + Gaussian noise.
    CC BY 4.0.


Brown_SIDD_chessboard_gray.png — 761×1012, uint16, 1.3 MB.
    Extracted from the SIDD dataset
    (Abdelhamed, Lin & Brown, CVPR 2018, Brown University). MIT License.
    Paper |
    Download portal



2D RGB Test Image



rgbtest.png — 512×512×3, uint8, 12 KB.
    Synthetic RGB test pattern, project-created. CC BY 4.0.



3D Fluorescence Microscopy Volumes



Myers_Tribolium_nGFP_0.1_0.2_0.5_20_13_late.tif
    — 48×773×665 (ZYX), uint16, 18 MB.
    Tribolium castaneum embryo expressing nuclear GFP, light-sheet microscopy.
    From the CARE training data
    (Myers Lab, MPI-CBG Dresden). CC0 1.0 (public domain).
    Weigert et al.,
    Nature Methods 2018


SPC0_TM0132_CM0_CM1_CHN00_CHN01.fusedStack.tif
    — 108×1352×532 (ZYX), uint16, 40 MB.
    Drosophila melanogaster embryo, dual-view light-sheet
    (SiMView).
    Keller Lab,
    Janelia Research Campus / HHMI. PI-confirmed redistribution.
    Tomer et al.,
    Nature Methods 2012


Royer_confocal_dragonfly_hcr_drerio_30somite_crop.tif
    — 75×3×444×331 (ZCYX), uint16, 45 MB.
    Zebrafish 30-somite embryo, spinning-disk confocal (Dragonfly), HCR fluorescence, 3 channels.
    Royer Lab, Chan Zuckerberg Biohub. CC BY 4.0.


Flybrain_3ch_mediumSize.tif
    — 294×3×768×768 (ZCYX), uint16, 501 MB.
    Adult Drosophila brain, 3-channel fluorescence volume.
    Janelia Research Campus / HHMI.
    PI-confirmed redistribution.


fixed_pattern_noise.tif
    — 73×400×340 (ZYX), uint16, 4.2 MB.
    Volume with fixed-pattern noise, acquired on a single-objective light-sheet
    microscope (soSPIM).
    Huang Lab (Bo Huang), UCSF.
    PI-confirmed redistribution.
    Gao et al.,
    Nature Methods 2015


C2-DrosophilaEggChamber-small.tif
    — 164×128×128 (ZYX), uint16, 3.5 MB.
    Drosophila egg chamber (cropped), point-scanning confocal.
    From the LimeSeg dataset.
    CC BY 4.0.
    Machado et al.,
    BMC Bioinformatics 2019



3D Fluorescence — OpenCell / Leonetti Lab

From the OpenCell project
(Manuel Leonetti Lab, Chan Zuckerberg Biohub) — CRISPR-tagged endogenous
proteins imaged in live human cells. CC BY-SA 4.0.
Cho et al., Science 2022.



Leonetti_p1H8_2_SNCA_PyProcessed_IJClean.tif
    — 46×2×1024×1024 (ZCYX), uint16, 139 MB.
    SNCA
    (α-synuclein).


Leonetti_OC-FOV_ARHGAP21_…_stack.tif
    — 106×600×600 (ZYX), uint16, 54 MB.
    ARHGAP21.


Leonetti_OC-FOV_ANKRD11_…_stack.tif
    — 106×600×600 (ZYX), uint16, 54 MB.
    ANKRD11.


Leonetti_p4B3_1_TM7SF2_PyProcessed_IJClean.tif
    — 35×2×1024×1024 (ZCYX), uint16, 106 MB.
    TM7SF2.


Leonetti_p1H10_2_SPTSSA_PyProcessed_IJClean.tif
    — 36×2×1024×1024 (ZCYX), uint16, 108 MB.
    SPTSSA.



2D+t Time-Lapse — Cognet Lab (Carbon Nanotube Tracking)

Near-infrared fluorescence imaging of single-walled carbon nanotubes (SWCNTs).
Cognet Research Group,
LP2N, University of Bordeaux / CNRS / IOGS. PI-confirmed redistribution.
Danial et al., ACS Nano 2019 |
Bhatt et al., Nano Letters 2022



Cognet_1-400fps.tif
    — 8000×320×320 (TYX), uint16, 797 MB.
    400 frames/s, NIR fluorescence.


Cognet_1-200fps.tif
    — 8000×320×320 (TYX), uint16, ~800 MB.
    200 frames/s, NIR fluorescence.


Cognet_1-100fps.tif
    — 8000×320×320 (TYX), uint16, 815 MB.
    100 frames/s, NIR fluorescence.


Cognet_r03-s01-100mW-20ms-175 50xplpeg-173.tif
    — 20000×80×80 (TYX), uint16, 182 MB.
    Single nanotube tracking, 20 ms exposure, PEGylated SWCNT.



3D+t and 4D Time-Lapse



Maitre_mouse blastocyst_fracking_180124_e3_crop.tif
    — 10×15×729×729 (TZYX), uint8, 55 MB.
    Mouse blastocyst, time-lapse light-sheet microscopy.
    Maitre Lab,
    Institut Curie.
    Dumortier et al.,
    Science 2019.
    CC BY-NC-SA 4.0; PI confirmed redistribution. Not available from
    any public repository — shared directly by the PI.


Hyman_HeLa.tif
    — 39×47×320×320 (TZYX), uint16, 120 MB.
    HeLa cell 4D dataset (39 time points, 47 Z-slices).
    Hyman Lab,
    MPI-CBG Dresden.
    PI-confirmed redistribution.






Datasets NOT included in this record

Downloaded at runtime by Aydin from original source URLs:



camera.png — “Cameraman” (MIT, 1978). CC BY-NC.
    MIT DOME

lizard.png — Berkeley
    BSDS300
    #87046. Non-commercial research only.

mandrill.tif —
    USC-SIPI 4.2.03. Copyright unknown.

OME-TIFF examples —
    openmicroscopy.org.






Compression

Large TIFFs (> 5 MB) losslessly re-compressed with Zstandard (zstd) +
horizontal predictor via tifffile.
Ratios: 1.3×–4.5×. Pixel data is bit-for-bit identical.
Readable by any TIFF reader supporting zstd.





Related software



Aydin on GitHub

Aydin on PyPI

Aydin documentation

Aydin software DOI
description: Per-file licensing notes:

- OpenCell/Leonetti data (5 files): CC BY-SA 4.0
  (Cho et al., Science 2022, DOI: 10.1126/science.abi6983)
  Browse at: https://opencell.czbiohub.org/
- CARE/Tribolium data: CC0 1.0 (public domain)
  (Weigert et al., Nature Methods 2018)
  Dataset DOI: 10.17617/3.FDFZOF
- LimeSeg/Machado egg chamber: CC BY 4.0
  (Machado et al., BMC Bioinformatics 2019)
  Original dataset: https://zenodo.org/records/1472859
- SIDD/Brown chessboard: MIT License
  (Abdelhamed et al., CVPR 2018)
  Dataset: https://abdokamel.github.io/sidd/
- Maitre blastocyst: CC BY-NC-SA 4.0 per original publication
  (Dumortier et al., Science 2019); PI confirmed redistribution.
  Not available from any public data repository.
- Periodic noise image: Apache 2.0 / BSD-3 (OpenCV)
- Pollen SEM: Public domain (Dartmouth Electron Microscope Facility)
  Source: http://remf.dartmouth.edu/images/botanicalPollenSEM/
- Andromeda: Public domain (Isaac Roberts, 1888)
- Gauss portrait, Mona Lisa, Characters: Public domain
- New York, Scaffoldings, RGB test, noisy NY: CC BY 4.0 (Royer)
- Fountain: Public domain / open access (U. Edinburgh)
- Cognet nanotube data: PI-confirmed redistribution
  Lab: https://www.cognet-research.com/
- Keller Dmel: PI-confirmed redistribution
  Lab: https://www.janelia.org/lab/keller-lab
  SiMView: https://www.janelia.org/open-science/simview
- Janelia Flybrain: PI-confirmed redistribution
- Hyman HeLa: PI-confirmed redistribution
  Lab: https://hymanlab.mpi-cbg.de/hyman_lab/
- Huang fixed pattern noise: PI-confirmed redistribution
  Lab: https://huanglab.ucsf.edu/ (Bo Huang, UCSF)
  Acquired on soSPIM (single-objective light-sheet microscope)
  Related: DOI 10.1038/nmeth.3402

These datasets are automatically downloaded by the aydin Python package (aydin.io.datasets module). The overarching CC-BY-4.0 license covers the collection as a whole; individual files retain their original licenses as noted above.