List of Data Sets

Dna-paint 

Storm

Several wells for each cell type were seeded in 96-well plates (Corning) and imaged over the course of 3–5 d, every 4 h using an Incucyte S3 Live-Cell Analysis system (Sartorius) equipped with its standard CMOS camera (Basler acA1920-155um). The Incucyte HD phase-contrast imaging algorithm allows visualization of phase delays produced by cells without the phase annulus or phase ring found in conventional Zernike phase images. Because of this, LIVECell phase-contrast images are characterized by less pronounced halo artifacts and more high-frequency content than other phase-contrast modalities. Phase-contrast images were acquired using a ×10 objective from two positions in each well adding up to a total of 1,310 images (1,408 × 1,040 pixels corresponding to 1.75 × 1.29 mm2) that were each cropped into four equally sized images (704 × 520 pixels corresponding to 0.875 × 0.645 mm2) that were then annotated.

Includes data from CLEM, TEM and STEM, EDX, ...

Volume EM

Large range of imaging modalities, ranging from wide-field, super resolution,.. to spatial DNA sequencing 

Both Brightfield with stains and fluorescence datasets of tissues

Contains 3D cryo-EM tomographs and maps, volume-em data sets , or hard and soft X-Ray tomography. FIB-SEM, SBF-SEM

It also contains CLEM Correlative Light Electron Microscopy experiments... See the experiment list EMDB < Search results (ebi.ac.uk) for full list of modalities.

From Brightfield slide scanning, with different stains. Available in tiff, svs or ndpi.

Only from Coherent X-Ray imaging

All Microscopy format accepted

Microscopy settings for each dataset are available by clicking on the "More Details Button"

Diverse microscopes (mostly light microscopy, but some electronic microscopy as well). SSBD tries to store and curate 4D datasets, ie images that are 3D together with time element. 

Diverse

Immunofluorescent sections were imaged on a Nikon AR1 confocal or Nikon Widefield CCD Microscope. Each confocal image is a composite of maximum projections, derived from stacks of optical sections.

There are 15 images. The images were acquired using a Nikon Eclipse TE200 microscope with a 20x, 0.45 NA objective lens and a 0.52 NA condenser lens, and are provided courtesy of the W.M. Keck 3D Fusion Microscope Facility at Northeastern University. Each image contains 640 x 480 pixels with an approximate size of 0.42 x 0.42 μm.

Two-photon imaging was performed using a galvanometer-based scanning system (Prairie Technologies, acquired by Bruker Inc.) on an Olympus BX61WI equipped with 60X water immersion objective (0.9 NA), using a Ti:sapphire laser (Coherent Inc.) controlled by PrairieView software at 910 nm. Z-stacks (0.3 μm axial spacing) from secondary or tertiary dendrites from CA1 neurons were collected every 5 min for up to 4 h. The field of view was 19.8 × 19.8 μm at 1024 × 1024 pixels.

The dataset was generated using the virtual microscope imitating the microscope Zeiss S100 (objective Zeiss 63x/1.40 Oil DIC) attached to confocal unit Atto CARV and CCD camera Micromax 1300-YHS.

The dataset was generated using the virtual microscope imitating the microscope Zeiss S100 (objective Zeiss 63x/1.40 Oil DIC) attached to confocal unit Atto CARV and CCD camera Micromax 1300-YHS

histopathology images  - 700X460 pixels,RGB 8-bit images stored as PNG

There are 10 fields of view of each sample, for a total of 50 fields of view. The images were acquired on a Zeiss Axiovert 200M microscope. The images provided here are a single channel, DNA. The image size is 512 x 512 pixels. The images are provided as 8-bit TIFF files.

Imaging varies by neuron type and species, includes:

1. Transmitted light brightfield
2. Confocal
3. in-vivo 2-photon laser scanning

Serial section Transmission Electron Microscopy (ssTEM).

Bright field microscopy