time-series

A complete package for fluorescence lifetime analysis implemented as an R package with sample data.

The wound healing tool measures the area of a wound in a time series of images of cellular tissue. The tool will measure the area of the wound, i.e. the area that does not contain tissue, in each image. The segmentation is based on the fact that the image is more homogeneous in the region of the wound as in the region of the tissue. Via the options, one of two methods to detect the empty area, can be selected. The first uses edge detection, the second a variance filter. Holes in the detected tissue are filled using morphological operations.

Part of ATLAS software

Comment / Instructions: 

You can upload your image at the Mobyle@SERPICO portal and download the result. The workflow is only available online, i.e. no download possible.

JFilament is an ImageJ plugin for segmentation and tracking of 2D and 3D filaments in fluorescenece microscopy images. The main algorithm used in Jfilament is "Stretching Open Active Contours" (SOAC). In order to use this method, the user must define seed points in the image where the SOAC method will begin.

JFilament also includes 2D "closed" active contours which can be used for tasks such as segmentation and tracking of cell boundaries.

Workflow of data-analysis strategies for image-based cell profiling.

1. Image analysis (image correction, image segmentation, feature extraction)
2. Image quality control
3. Preprocessing extracted features
4. Dimensionality reduction
5. Single-cell data aggregation
6. Measuring profile similarity
7. Assay quality assessment
8. Downstream analysis

Examples of publications where the workflow has been used at least partly:

• Image-based multivariate profiling of drug responses from single cells
• Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes
• Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping
• Cell shape and the microenvironment regulate nuclear translocation of NF‐κB in breast epithelial and tumor cells
• Genome-wide RNAi Screening Identifies Protein Modules Required for 40S Subunit Synthesis in Human Cells
• Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
• Systematic morphological profiling of human gene and allele function via Cell Painting