haesleinhuepf / Fiji-Napari-Dictionary

Fiji-Napari-Dictionary

This document contains translations of typical terms, menus and simple workflows in Fiji and their counterparts in Napari together with links to documentation, plugins and example code. Feedback is welcome as github issue, contributions and suggestions can be sent as pull-request.

The dictionary lists things alphabetically in this form as

• ImageJ / Fiji thing (menu)
  • Napari thing (menu, plugin)

Use the browsers search function (CTRL+F or CMD+F) to find things.

Dictionary

• Analyze > Analyze Particles (menu)

  • Plugins > morphometrics > Measure region properties (menu, available as plugin)
  • Tools > Measurement > Label Statistics (menu, available as plugin)
  • Tools > Measurement > Measurements (menu, available as plugin)
  • Tools > Measurement > Regionprops (menu, available as plugin)

• Analyze > Plot Profile (menu)

  • Tools > Measurement > Plot profile (menu, available as plugin)

• Edit > Copy to system (menu)

  • File > Copy Screenshot to Clipboard (menu)

• Edit > Invert (menu)

  • Tools > Image math > Invert image (menu, available as plugin 1, plugin 2)

• File > New > Script (menu)

  • Tools > Scripts > Script Editor (menu, available as plugin)

• Image > Adjust > Brightness / contrast (menu)

  • Right-click on contrast slider (popup dialog)
  • Tools > Visualization > Brightness / contrast (menu, available as plugin)

• Image > Adjust > Threshold (menu)

  • Tools > Segmentation / Binarization > Threshold ... (menu, menu / button, available as plugin 1, plugin 2, plugin 3)
  • Tools > Utilities > Assistant, Binarize (menu / button, available as plugin 1, plugin 2, plugin 3)

• Image > Color > Split Channels

  • Right-click on layer list > Split RGB (popup menu)

• Image > Crop (menu)

  • Plugins > napari-nd-cropper: nd_ Cropper (menu, availablee as plugin)
  • Tools > Utilities > Crop Region (menu, available as plugin)

• Image > Duplicate (menu)

  • (Right-click on Layer) > Duplicate Layer (popup menu)
  • Tools > Utilties > Duplicate current timepoint (menu, available as plugin)

• Image > Stacks > Stack to Hyperstack (menu)

  • Tools > Utilities > Convert 3D stack to 2D timelapse (menu, available as plugin)

• Image > Stacks > Tools > Reduce (menu)

  • Tools > Utilities > Assistant, Projection (menu / button, available as plugin)

• Image > Stacks > Plot Z-Axis-Profile (menu)

  • Plugins > napari-time-series-plotter: TSPExplorer (menu, availablee as plugin)

• Image > Stacks > Z-Project (menu)

  • Plugins > napari-math > ... (menu, available as plugin)
  • Right-click on image layer > Make Projection > ... (popup menu)
  • Tools > Utilities > Assistant, Projection (menu / button, available as plugin)

• Image > Transform > ... (menu)

  • Plugins > napari-manual-transforms: Rotation Helper (menu, available as plugin)
  • Tools > Utilities > Assistant, Transform (menu / button, available as plugin)

• Image > Properties (menu)

  • Tools > Utilities > Layer Details (menu, availabla as plugin)
  • Tools > Utilities > Set voxel size (menu, available as plugin)

• Fiji (plugin collection)

  • devbio-napari (plugin collection, available as plugin)

• Lookup table / LUT (term)

  • Colormap (code example 1, example 2)

• Plugins › 3DSuite › Segmentation › 3D Watershed (menu, plugin)

  • Plugins > Segmentation / labeling > Local minima seeded Watershed (menu, available as plugin 1)

• Plugins > Macros > Record (menu)

  • Plugins > Utilities > Assistant (menu, available as plugin, documentation)

• Plugins > Registration > StackReg (menu, plugin)

  • Plugins > napari-pystackreg: pystackreg (menu, available as plugin)

• Plugins > Segmentation > Trainable (Weka) Segmentation (menu, available as plugin)

  • Plugins > hesperos > OneShot segmentation (menu, available as plugin)
  • Plugins > napari-buds > bud annotation (menu, available as plugin)
  • Tools > Segmentation / labeling > Object Segmentation (menu, available as plugin)

• Process > Binary > Erode / Dilate / Open / Close (menu)

  • Tools > Segmentation post-processing > Binary ... (menu, available as plugin)
  • Tools > Utilities > Assistant, Binarize (menu / button, available as plugin 1, plugin 2, plugin 3)

• Process > Binary > Fill holes (menu)

  • Tools > Segmentation post-processing > Binary Fill Holes (menu, available as plugin)

• Process > Binary > Skeletonize (menu)

  • Tools > Segmentation post-processing > Skeletonize (menu, available as plugin)

• Process > Binary > Watershed (menu)

• Tools > Segmentation post-processing > Split touching objects (menu, available as plugin 1)

• Tools > Segmentation / labeling > Touching objects labeling (menu, plugin 2)

• Process > Filter > Gaussian Blur / 3D (menu)

  • Tools > Filtering / noise removal > Gaussian (menu, available as plugin 1, plugin 2, plugin 3)

• Process > Filter > Median / 3D (menu)

  • Tools > Filtering / noise removal > Median (menu, available as plugin 1, plugin 2, plugin 3)

• Process > Find Maxima... (menu)

  • Plugins > napari-blob-detection > Detect blobs on images (menu, available as plugin)

• Process > Find Edges... (menu)

  • Tools > Filtering / edge enhancement > ... (menu, available as plugin 1, plugin 2, plugin 3)

• Process > Image Calculator (menu)

  • Plugins > napari-math > ... (menu, available as plugin)
  • Tools > Image math > ... (menu, available as plugin
  • Tools > Utilities > Assistant, Combine (menu / button, available as plugin)

• Process > Subtract background (menu)

  • Tools > Filtering / background removal > Rolling ball (menu, available as plugin)
  • Tools > Filtering / background removal > Black / white top hat (menu, available as plugin 1, plugin 2, plugin 3)