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.

SynActJ

Workflow
Description

SynActJ (Synaptic Activity in ImageJ) is an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using an R Shiny workflow. 

has topic
Live sample imaging
has function
Neuron image analysis
SynActJ workflow

ASTEC

Collection
Workflow
Description

ASTEC stands for Adaptive Segmentation and Tracking of Embryonic Cells. It proposes a full workflow for time lapse light sheet imaging analysis, including drift/motion compensation before the segmentation itself, and the capacity to correct for it.  It was used to process 3D+t movies acquired by the MuViSPIM light-sheet microscope in particular.

has topic
Light-sheet microscopy
has function
Cell segmentation
Drift correction
Astec embryon

Voxelytics-Align

Workflow
Description

Voxelytic-Align is a commercial software provided as a service on cloud targetted to electron microscopy reconstruction (alignement, artifact correction...)

has topic
Electron microscopy
Serial block-face scanning electron microscopy
has function
Alignment construction
Image reconstruction
Image stitching

Lecture Bio-image analysis, biostatistics, programming and machine learning for computational biology at the Biotechnology Center, TU Dresden, 2021

Thie lecture is for Python beginners who want to dive into image processing with Python. It specifically aims for students and scientists working with microscopy images in the life sciences. We start with python basics, dive into descriptive statistics for working with measurements and matplotlib for plotting results.

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