SciGet

SciGet Microscopy Webapps

Run Microscopy Tools in Your Browser

Segment nuclei and stream, view and measure large microscopy images in your browser without uploading your data.

5 apps across 3 categories

01

Registration & Normalization

Align images with each other or with a standard template.

Registration & Normalization

elastix

Rigid, affine and B-spline registration with elastix.

  • MRI, CT, Microscopy
  • DICOM, NIfTI, OME-Zarr, TIFF, NRRD/MHA/MINC
  • No GPU needed
  • Command line

02

Microscopy

Explore microscopy images, segment cells and analyse calcium signals.

Microscopy

ZARRo

Stream, view and measure large OME-Zarr images.

  • Microscopy
  • OME-Zarr
  • No GPU needed
 Microscopy

StarDist

Segment cell nuclei in 2D fluorescence microscopy.

  • Microscopy
  • TIFF
  • No GPU needed
 Microscopy

Calcium imaging

Two-photon motion correction, ROIs, ΔF/F and spikes

  • Brain · Microscopy
  • TIFF
  • No GPU needed
 Microscopy

Spot detection

Detect smFISH spots in 2D and 3D microscopy images.

  • Microscopy
  • TIFF
  • No GPU needed

03

Visualization

Explore large volumes and surfaces and make slice videos.

Visualization

ZARRo

Stream, view and measure large OME-Zarr images.

  • Microscopy
  • OME-Zarr
  • No GPU needed