Bioinformatics Software

Quantitative Image Analysis Tools

Below is a list of bioinformatics software developed by Houston Methodist’s Department of Systems Medicine and Bioengineering.

Zebrafish Image Quantitator (ZFIQ)
ZFIQ is a user-friendly software package that is designed for quantitative Zebrafish image analysis, whose key features include automated cell detection, segmentation, quantification and phenotype classification.

Neuron Image Quantitator (NeuronIQ)
The NeuronIQ software is designed to be a user-friendly package for quantitative neuron image analysis, whose key features include automated dendrite and spine detection, quantification, and spine phenotype classification.

Neurite Image Quantitator (NeuritelQ)
Designed for quantitative neurite image analysis, this user-friendly NeuriteIQ software package’s key features include automated neurite labeling and quantification of their length and brightness.

Dynamic Cell Image Quantitator (DCellIQ)
This user-friendly DCellIQ software package is designed for quantitative time-lapse nuclei image analysis for cell cycle studies, whose key features include automated nuclei detection, segmentation, quantification, tracking, cell cycle phase identification and statistical analysis of the cell cycle duration.

Genomic Cell Image Quantitator (GCellIQ)
The GCellIQ open-source software package is user-friendly and aims to provide an automated pipeline for processing large volumes of digital images generated from high-content screening (HCS), including those by RNAi or small compound screening. It is suitable for batch processing large image datasets with little human interference.

The AxonTracker 3-D software is useful for semi-automatically tracking and labeling axon structures from the motor axon connectome datasets. It is a parameter-free software and, hence, can be used over a broad range of datasets.

Assisted Follow-up in NeuroImaging of Therapeutic Intervention (AFINITI)
AFINITI is a user-friendly software package for volumetrics measurement of human brain tumor. The key functions are semi-automatic brain tumor segmentation and quantitative tumor growth follow-up.