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.

EB1 tracking with IJ

Submitted by Perrine on Mon, 04/08/2019 - 11:00

We take an example image data of microtubule binding protein EB1, and will study how to automatically track those signals and how to analyze the tracking results. We use ImageJ for measuring the temporal changes in signal positions, and will feed the tracking results for analyzing their dynamics using Matlab in the following session EB1 tracking with Matlab.

Automated workflow for parallel Multiview Reconstruction

Workflow
Description

Automated workflow for performing multiview reconstruction of large multiview, multichannel, multiillumination time-lapse SPIM data on a high performance computing (HPC) cluster or on a single workstation. 

has topic
Light-sheet microscopy
has function
Image registration
Image deconvolution
Selective plane illumination microscopy reconstruction
Image processing
Drift correction

Nuclei Segmentation (ilastik)

Workflow
Description

NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python post-processing.

has topic
Machine learning
has function
Pixel classification
need a thumbnail

Nuclei Segmentation (Mask-RCNN)

Workflow
Description

NEUBIAS-WG5 workflow for nuclei segmentation using Mask-RCNN. The workflow uses Matterport Mask-RCNN. Keras implementation. The model was trained with Kaggle 2018 Data Science Bowl images.

has topic
Machine learning
has function
Image segmentation
Object detection
need a thumbnail
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