- View a dataset in napari v0.4.16An Album solution for displaying a dataset with napari.napari contributors (2019). napari: a multi-dimensional image viewer for python.
![A dataset displayed in napari.]()
- 3D image mesh generatorScikit based mesh generation from pixel data, either saved as STL file or displayed via vtkplotlib.
![Screenshot of a raw image next to the mesh generated from it and displayed using vtlplotlib.]()
- CellSketch: Plot analysis resultsThis solution plots exemplary spatial analysis results of a CellSketch project.A. Müller, D. Schmidt, C. S. Xu, S. Pang, J. V. D’Costa, S. Kretschmar, C. Münster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039.
![Plots generated by this solution.]()
- CellSketch: Display exported meshesDisplays all exported meshes from a CellSketch project using vtlplotlib. Colors can be adjusted in the CellSketch BigDataViewer app.
![Screenshot of a raw image next to the mesh generated from it and displayed using vtlplotlib.]()
- CellSketch: Export masks and labelmaps as meshesVTK based mesh generation from pixel data, exports all masks and labelmaps from CellSketch project as meshes.
![Screenshot of a raw image next to the mesh generated from it and displayed using vtkplotlib.]()
- Launch Blender 3.3.1This solution launches Blender, optionally with a specific .blend file as input.Blender Online Community: Blender - a 3D modelling and rendering package (2018). Stichting Blender Foundation, Amsterdam.
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- CellSketch: Create new projectThis solution creates a new CellSketch project by importing the raw dataset as well as masks and labelings of cell components.A. Müller, D. Schmidt, C. S. Xu, S. Pang, J. V. D’Costa, S. Kretschmar, C. Münster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039.Pietzsch, T., Saalfeld, S., Preibisch, S., & Tomancak, P. (2015). BigDataViewer: visualization and processing for large image data sets. Nature Methods, 12(6), 481–483.
![These are exemplary masks which this solution imports into a joint BDV project.]()
- CellSketch: Add labelmapThis solution adds a labelmap to an existing CellSketch project.A. Müller, D. Schmidt, C. S. Xu, S. Pang, J. V. D’Costa, S. Kretschmar, C. Münster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039.
- CellSketch: Add maskThis solution adds a mask to an existing CellSketch project.A. Müller, D. Schmidt, C. S. Xu, S. Pang, J. V. D’Costa, S. Kretschmar, C. Münster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039.
- CellSketch: Run spatial analysisThis solution performs spatial analysis for all organelles in a CellSketch project.A. Müller, D. Schmidt, C. S. Xu, S. Pang, J. V. D’Costa, S. Kretschmar, C. Münster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039.Pietzsch, T., Saalfeld, S., Preibisch, S., & Tomancak, P. (2015). BigDataViewer: visualization and processing for large image data sets. Nature Methods, 12(6), 481–483.
![TODO]()
- CellSketch: Generate Blender scene from mesh filesThis solution imports STL files from a CellSketch project into the same scene, optionally reducing their mesh complexity and rendering the scene.Blender Online Community: Blender - a 3D modelling and rendering package (2018). Stichting Blender Foundation, Amsterdam.
- CellSketch: Display data in BigDataViewerThis solution displays a CellSketch project in BDV.A. Müller, D. Schmidt, C. S. Xu, S. Pang, J. V. D’Costa, S. Kretschmar, C. Münster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039.Pietzsch, T., Saalfeld, S., Preibisch, S., & Tomancak, P. (2015). BigDataViewer: visualization and processing for large image data sets. Nature Methods, 12(6), 481–483.
![TODO]()
- macrophage-brain-vasculature mbv_parent solutionA set of solutions for localizing macrophages, segmenting brain vasculature, and tumors
- macrophage-brain-vasculature find 3D points from 2D annotations solutionA solution for finding 3D coordinates from 2D annotations with respect to a target image
![Annotation of Macrophage signal intensities]()
- A Solution to run the polarityjam feature extraction pipelineA Solution to run the polarityjam Feature Extraction Pipeline.Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification
![Polarityjam cover image]()
- Polarityjam R-Shiny App SolutionA Solution to run the Polarityjam R Shiny App.Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification
![Polarityjam app cover image]()
