time-series

Quantitative Criterion Acquisition Network (QCA Net) performs instance segmentation of 3D fluorescence microscopic images. QCA Net consists of Nuclear Segmentation Network (NSN) that learned nuclear segmentation task and Nuclear Detection Network (NDN) that learned nuclear identification task. QCA Net performs instance segmentation of the time-series 3D fluorescence microscopic images at each time point, and the quantitative criteria for mouse development are extracted from the acquired time-series segmentation image. The detailed information on this program is described in our manuscript posted on bioRxiv.

LibTIFF - TIFF Library and Utilities. This software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data. libtiff is a library, for reading and writing TIFF, a small collection of tools for doing simple manipulations of TIFF images.

Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.

Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji). 

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis.