Component

A Component is an implementation of certain image processing / analysis algorithms.

Each component alone does not solve a Bioimage Analysis problem.

These problems can be addressed by combining such components into workflows.

Batch_Filter_CaseStudy part 2

Submitted by Perrine on Mon, 04/08/2019 - 10:47

We will cover the theory behind some useful image preprocessing operations such as filtering for image restoration and feature enhancements, illumination compensation and background correction. We will then combine these operations and write a complete image analysis macro including image correction and 2D stitching of images coming from a large multiposition experiment.

EvaluateSegmentation Tool

Component
Description

A command line tool that allows to quantitatively compare two volumes of binary segmentations. Implements 22 different metrics for comparing segmentations such as Dice Coefficient, Hausdorff Distance and average Distance. 

Snakemake

Component
Description

A Python based workflow management software that allows to create workflows that seamlessly scale from a single workstation to a high performance computing cluster or cloud environments. 

YeastSpotter

Component
Description

Code to segment yeast cells using a pre-trained mask-rcnn model. We've tested this with yeast cells imaged in fluorescent images and brightfield images, and gotten good results with both modalities. This code implements an user-friendly script that hides all of the messy implementation details and parameters. Simply put all of your images to be segmented into the same directory, and then plug and go.

has topic
Bioimage informatics
has function
Cell segmentation
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