- 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: 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.Pape, C. (2019). constantinpape/z5
![TODO]()
- 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.
![cellsketch-pixel-view cover image]()
- 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: Add boundaryThis solution adds cell boundary (a filled 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: Add KNOSSOS filamentThis solution adds a KNOSSOS filament XML file 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.
- ilastik-LauncherAn album solution to run ilastikBerg, S., Kutra, D., Kroeger, T. et al. ilastik: interactive machine learning for (bio)image analysis. Nat Methods 16, 1226-1232 (2019).
![Logo of the ilastik suite.]()
- CellSketch: Export masks and labelmaps as meshesVTK based mesh generation from pixel data, exports all masks and labelmaps from CellSketch project as meshes.Schroeder, W.; Martin, K.; Lorensen, B. (2006). The Visualization Toolkit (4th ed.), Kitware, ISBN 978-1-930934-19-1Pape, C. (2019). constantinpape/z5
![Screenshot of a raw image next to the mesh generated from it and displayed using vtkplotlib.]()
- CellSketch: Display exported meshesDisplays all exported meshes from a CellSketch project using vtkplotlib. Colors can be adjusted in the CellSketch BigDataViewer app.Schroeder, W.; Martin, K.; Lorensen, B. (2006). The Visualization Toolkit (4th ed.), Kitware, ISBN 978-1-930934-19-1Pape, C. (2019). constantinpape/z5
![Screenshot of a raw image next to the mesh generated from it and displayed using vtkplotlib.]()
- 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: 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.
![This rendering was generated based on data from the following publication: Andreas Müller, Deborah Schmidt, C. Shan Xu, Song Pang, Joyson Verner D'Costa, Susanne Kretschmar, Carla Münster, Thomas Kurth, Florian Jug, Martin Weigert, Harald F. Hess, Michele Solimena; 3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039. doi: https://doi.org/10.1083/jcb.202010039]()
- 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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- StarDist TrainAn album solution to train a stardist modelUwe Schmidt and Martin Weigert and Coleman Broaddus and Gene Myers, Cell Detection with Star-Convex Polygons, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Granada, Spain, September 2018Martin Weigert and Uwe Schmidt and Robert Haase and Ko Sugawara and Gene Myers, Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy, IEEE Winter Conference on Applications of Computer Vision (WACV), March 2020
![StarDist Train Cover Image]()
- StarDist PredictAn album solution to run stardist to predict 3D segmentation masks.Uwe Schmidt and Martin Weigert and Coleman Broaddus and Gene Myers, Cell Detection with Star-Convex Polygons, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Granada, Spain, September 2018Martin Weigert and Uwe Schmidt and Robert Haase and Ko Sugawara and Gene Myers, Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy, IEEE Winter Conference on Applications of Computer Vision (WACV), March 2020
![StarDist Predict Cover Image]()
- CSBDeep Unet TrainAn album solution to train a Unet with CSBDeep.Weigert, Martin, et al. "Content-aware image restoration: pushing the limits of fluorescence microscopy." Nature methods 15.12 (2018): 1090-1097.
![CSBDeep Unet Train Cover Image]()
- CSBDeep Unet PredictAn album solution to predict your image from a Unet with the csbdeep_unet_train solution.Weigert, Martin, et al. "Content-aware image restoration: pushing the limits of fluorescence microscopy." Nature methods 15.12 (2018): 1090-1097.
![CSBDeep Unet Predict Cover Image]()
