Author: David Dang, PhD at Draviam Lab (School of Biological and Chemical Sciences, Queen Mary University of London) and Sastry Group (Department of Computer Science, King's College London)
SpinX Software is designed to study dynamics of subcellular structures in 3D time-resolved movies (e.g. spindle and cell cortex). The SpinX framework is composed of four modules:
| Name | Type | Description | Output |
|---|---|---|---|
| spinx_ai_module_pred_spindle | Folder | SpinX AI prediction module to segment spindle | Segmentation mask of spindles |
| spinx_ai_module_pred_cell_cortex | Folder | SpinX AI prediction module to segment cell cortex | Segmentation mask of cell cortex |
| spinx_3d_modelling_module | Folder | SpinX 3D reconstruction and modelling module | Figures and measurement table .csv) |
General notes:
SpinX supports as input list of files (.png, .tif) or multi-page .OME-TIFF files. Each module contains a requirement.txt with detailed information on used dependancies. SpinX requires the installation of Mask R-CNN (Matterport: https://github.com/matterport/Mask_RCNN).
Folder Structure for SpinX AI prediction module to segment spindle and cell cortex:
├── input # List of files (Example images)
├── input_ome_tiff # OME-TIFF (Example multi-page OME-TIFF)
├── mrcnn # Mask R-CNN
├── samples # Information on trained neural network
├── output # This folder will be generated automatically
Folder Structure for SpinX 3D reconstruction and modelling module:
├── input # List of files (Example images)
├── cell_cortex # Segmentation mask of cell cortex (predicted by the previous module)
├── spindle # Segmentation mask of spindle (predicted by the previous module)
├── input_ome_tiff # OME-TIFF (Example multi-page OME-TIFF)
├── cell_cortex # Segmentation mask of cell cortex (predicted by the previous module)
├── spindle # Segmentation mask of spindle (predicted by the previous module)
├── font # Font file for plotting
├── output # This folder will be generated automatically.