MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

SLDC (Segment Locate Dispatch Classify)


SLDC is an open-source Python workflow. SLDC stands for Segment Locate Dispatch Classify. This framework aims at facilitating the development of algorithms for detecting objects in multi-gigapixel images. Particularly, it provides algorithm developers with a structure to define problem-dependent components of their processing workflow (i.e. segmentation and classification) in a concise way. Every other concern such as parallelization and large image handling are encapsulated by the framework. It also features a powerful and customizable logging system and some components to apply several workflows one after another on a same image. SLDC can work on local images or interact with Cytomine

Example image:

Toy image data

has topic

classification of hemp fibers based on morphological features



In this workflow, you can use MorphoLibJ to generate accurate morphometric measurements

  • First the fibers are segmented by mathematical morphology:
    • for example by using MorphoLibJ:
      • Create a marker image by creating a rough mask with extended regional maxima (similar to Find Max), such that you have one max per fiber
      • Use the marker controlled watershed (in MorpholLibJ/ Segmentation/ marker controlled watershed) : indicate the original grayscale image as the input, Marker will be your maxima image, select None for mask
      • it will create a label mask of your fibers
  •  In MorphoLibJ /analyze/ select Region Morphometry: this will compute different shape factors which are more robust than the ones implemented by default in ImageJ
  • Export the result table created to a csv file
  • Then for example in Matlab or R, you can apply a PCA analysis (Principal component analysis) followed by a k-means with the number of class (clusters) (different fibers type) you want to separate.
  • You can then add this class as a new feature to your csv file.
  • From this you can sort your labelled fibers into these clusters for a visual feedback or further spatial analysis
has topic
hemp analysis

Volocity - 3D Object Segmentation and Tracking


In the commercial image analysis software "Volocity", automated measurement protocols can be constructed by dragging, dropping and configuring a sequence of individual "tasks".

By combining the "Find Objects" task with a subsequent "Track" task, 3D objects can be identified and followed over time. The initial "Find Objects" segmentation can be refined, e.g. using "Separate Touching Objects"; and tracking results in the form of "Measurement Items" can be viewed in tabular form, as a graph, etc.