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Lund University

Microscopy-Based High-Content Screening (High-Content Imaging): Software and tools

Literature, tools and other resources for microscopy-based high-content screening (HCS), also referred to as high-content analysis (HCA) or high-content imaging (HCI). Covered areas include microscopy theory, screening procedures, image analysis, phenotyp

BISE

http://www.biii.eu/

Search engine for image analysis tools

 

CellProfiler and CellProfiler Analyst

http://cellprofiler.org/

Free image analysis software

Video tutorials: https://www.youtube.com/watch?v=dKAJoxMoZz0&list=PLeM_d8ZXiMCP1el4oT591FQWlF2FdSfMN

 

Fiji

https://fiji.sc/

Free image analysis software based on ImageJ

Video tutorials for Fiji and ImageJ: https://www.youtube.com/watch?v=KoqpCsha-UU&list=PLeM_d8ZXiMCOYmpf92IBfOpQQBduWuiw7

 

ImageJ

https://imagej.nih.gov/ij/

Free image analysis software

 

Ilastik

http://ilastik.org/

Free image analysis software

Video tutorials: https://www.youtube.com/watch?v=N-QhiTWVDmk&list=PLeM_d8ZXiMCNXtVFvwAW23yXfTDsGFk5t

 

Advanced Cell Classifier

http://www.cellclassifier.org/

Free image analysis software

Video tutorials: https://www.youtube.com/watch?v=7RhmAPCWIgw&list=PLeM_d8ZXiMCMUmeWSO3HwvhPXst_-0kkj

 

Cell Tracker

https://warwick.ac.uk/fac/sci/dcs/people/till_bretschneider/celltracker

Free oftware for tracking nuclear and cytoplasmic fluorescence intensities from live cell microscopy time series data

Video tutorials: https://www.youtube.com/watch?v=onigTWCRkyE&list=PLeM_d8ZXiMCPW3Z8PoGowwhduxyGzATcV

 

OMERO: https://www.openmicroscopy.org/omero/

Free software for image data management

Video tutorials: https://www.youtube.com/watch?v=xCZH8teyBOk&list=PLeM_d8ZXiMCNHTEwTK8QCpTICi2xJvmXO