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.

Nuclei Segmentation (CellProfiler)

Description

This workflow processes a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It was developed as a test workflow for Neubias BIAFLOWS Benchmarking tool.

has function

Nuclei Tracking (ImageJ)

has function
need a thumbnail

Nuclei Segmentation (Python)

Description

This workflow processes images of cells with discernible nuclei and outputs a binary mask containing where nuclei are detected.

need a thumbnail

Spot Detection (Icy)

has function
need a thumbnail

Spot Detection 3D (ImageJ)

Description

This workflow detects spots from a 3D image by using straightforward set of ImageJ components. It receives the Laplacian Radius and the Threshold  value s input.

has function
need a thumbnail

Spot detection (ImageJ)

Description

This workflow detects spots from a 2D image by using straightforward set of ImageJ components. It receives the Laplacian Radius and the Noise tolerance as input.

has function
need a thumbnail

Filament Tracing (ImageJ)

need a thumbnail

3D colocalisation

Bioimage Analyst
Developer

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

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