Drosophila melanogaster

Description

Open source deep learning based framework for multi-animal pose tracking. It can track animal and any number of animals and has a labeling/training GUI for learning and proofreading.

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Description

Algorithm and software created to extract animal trajectories from videos of a collection of animals up to 100 individuals. Idtrackerai uses two convolutional networks: one for animal identification and another to detect when animals touch or cross each other.

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Description

Collection of several basic standard image segmentation methods focusing on medical imaging. In particular, the key block/applications are (un)supervised image segmentation using superpixels, object centre detection and region growing with a shape prior. Besides the open-source code, there is also a few sample images.

 

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BBBC002v1

Submitted by sampaio on Tue, 02/05/2019 - 10:12

Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2) has a different gene knocked down by RNAi.

The sample preparation is described in more detail by [Carpenter et al. (Genome Biology, 2006)(http://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-10-r1…)

Description

AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

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