Time lapse SPIM processing software tools | Single plane illumination microscopy image analysis
Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications.
An automated workflow for processing large multiview, multi-channel, multi-illumination time-lapse selective plane illumination microscopy (SPIM) data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it.
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
Performs interactive segmentation and investigation of 3D+t microscopy datasets containing cell boundary information. CellECT allows users to add, delete, or modify segments. It offers an adaptive confidence metric assisting users in the recognition of areas of uncertain segmentation. This tool enables the detection of spurious boundaries and can suggest corrections. Moreover, it can be useful for assessing the quality of segmentations and the efficiency of the available metrics.
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