SciGet

Preclinical Webapps

Run Preclinical Imaging Tools in Your Browser

Convert, view, denoise and register small-animal MRI, map susceptibility, and analyse light-sheet, two-photon and neuron data in your browser without uploading your data.

15 apps across 10 categories

01

Quantitative MRI

Compute quantitative tissue maps and measure blood flow.

Quantitative MRI

QSMbly

Make QSM, R2* and SWI maps from multi-echo MRI.

  • Brain · MRI
  • DICOM, NIfTI
  • No GPU needed
  • Command line

02

Diffusion & Tractography

Fit diffusion models and reconstruct white-matter pathways.

Diffusion & Tractography

Degibbs

Remove Gibbs ringing from MRI scans.

  • MRI
  • DICOM, NIfTI
  • No GPU needed
  • Command line
 Diffusion & Tractography

Dwidenoise

Denoise diffusion MRI with Patch2Self.

  • MRI
  • DICOM, NIfTI
  • No GPU needed
  • Command line

03

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
 Registration & Normalization

Tile stitching

Stitch overlapping 2D and 3D microscopy tiles

  • Microscopy
  • TIFF
  • No GPU needed

04

Preprocessing

Prepare images with correction, denoising, brain extraction and image maths.

Preprocessing

NiiMath

Apply image maths, filters and meshing with niimath.

  • MRI, CT
  • DICOM, NIfTI
  • No GPU needed
  • Command line
 Preprocessing

Degibbs

Remove Gibbs ringing from MRI scans.

  • MRI
  • DICOM, NIfTI
  • No GPU needed
  • Command line
 Preprocessing

Dwidenoise

Denoise diffusion MRI with Patch2Self.

  • MRI
  • DICOM, NIfTI
  • No GPU needed
  • Command line
 Preprocessing

ANTs DenoiseImage

Reduce noise in 3D MRI with ANTs adaptive non-local means.

  • MRI
  • DICOM, NIfTI
  • No GPU needed

05

Conversion

Convert scanner DICOM files to NIfTI and BIDS datasets.

Conversion

dcm2niix

Convert scanner DICOM exports to anatomical and DWI BIDS.

  • MRI
  • DICOM
  • No GPU needed

06

Fibre Orientation

Map fibre orientation and coherency in tissue images.

Fibre Orientation

Structure Tensor

Map fibre orientation and coherency in microscopy images.

  • Microscopy
  • TIFF, NIfTI
  • No GPU needed

07

Morphometry

Measure neuronal shape, branching and Sholl profiles.

Morphometry

NeuroMorph

Check SWC neurons and measure morphology and Sholl.

  • Brain · Microscopy
  • SWC
  • No GPU needed

08

Calcium Imaging

Correct motion, extract cell signals and infer activity from calcium imaging.

Calcium Imaging

Calcium imaging

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

  • Brain · Microscopy
  • TIFF
  • No GPU needed

09

Visualization

Explore large volumes and surfaces and make slice videos.

Visualization

MRI2VID

Convert DICOM, NIfTI or MGZ volumes into scrolling videos.

  • MRI, CT
  • DICOM, NIfTI, MGZ
  • No GPU needed
  • Command line
 Visualization

ZARRo

Stream, view and measure large OME-Zarr images.

  • Microscopy
  • OME-Zarr
  • No GPU needed
 Visualization

DICOM View

Browse DICOM series, images, headers and protocol.

  • MRI, CT
  • DICOM
  • No GPU needed

10

Quality Control

Check image quality and compare acquisition protocols.

Quality Control

dicompare

Check DICOM acquisitions against a reference protocol.

  • MRI
  • DICOM
  • No GPU needed
  • Command line
 Quality Control

DICOM View

Browse DICOM series, images, headers and protocol.

  • MRI, CT
  • DICOM
  • No GPU needed