Workflow

A workflow is a set of components assembled in some specific order to

  1. Measure and estimate some numerical parameters of the biological system or
  2. Visualization

for addressing a biological question. Workflows can be a combination of components from the same or different software packages using several scripts and manual steps.

Spot detection (ImageJ)

Workflow
Description

This workflow detects spots in a 2D image by filtering the image by Laplacian of Gaussian (user defined radius) and detecting regional intensity minima (user defined noise tolerance).

has function
Spot detection
need a thumbnail

Filament Tracing (ImageJ)

Workflow
has function
Filament tracing
Smoothing
Skeletonisation
need a thumbnail

3D object based colocalisation

Submitted by Perrine on Fri, 02/22/2019 - 09:21

A user comes to the Facility: “I’ve got a set of 2 channels 3D images where objects are overlapping. I think the overlap might not be the same from object to object. I would like to quantify the physical overlap and get a map of quantifications”. Your mission: write the appropriate macro, knowing a user might always change her/his mind, and ask for more… Ready to take on the challenge ?

autoQC

Collection
Workflow
Description

autoQC encapsulates a number of routines for performing microscope quality controls. From a few input images, it generates computer-friendly (i.e. CSV) data with numerical parameters for quality measures (resolution, field of view illumination, chromatic shift, stage reproducibility).

need a thumbnail

Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ)

Workflow
Description

The macro will segment nuclei and separate clustered nuclei in a 3D image using a distance transform watershed. As a result an index-mask image is written for each input image.

has function
Image segmentation
Watershed segmentation
Smoothing
need a thumbnail
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