Press Shift-1, Shift-2, … to add / remove the source to the view. In fused mode, several sources are overlaid.
In this dialog you can adjust the min & max for each source, select to what sources these min & max apply and pick a color for each source. Only the orientation of the bookmark will be restored. Bookmarks are saved in display settings file. A bookmark stores the position, zoom and orientation in the view but not the time-point. Shift-B then press any key to store a bookmark with this key as name. The view will zoom and unzoom around the mouse location. The view will rotate around the location you clicked.Ĭontrol-shift mouse-wheel or Command-mouse-wheel. Align with XZ plane: Shift-C or Shift-Y The view will rotate around the location you clicked. Press and hold shift to move faster, control to move slower.Ĭlick and drag. Moving around and display in BDV windows. The keyboard shortcuts listed below are valid for the default key-map. TrackScheme automatically adapts the level of detail while displaying data at varying scales. Level of detail to display large number of objects. User interactions with tracking objects rely on Kd-tree search on convex polytopes. Mastodon-graph is a graph library based on mastodon-collections, that underlies the data model of Mastodon.Įfficient retrieval of objects in space and time. Mastodon-graph: a data structure based on mastodon-collection, and optimized for lineage and tracking data. Mastodon-collection also offers techniques to do garbage-collection-free manipulations in Java, considerably improving the responsiveness of applications based on it. Thanks to CPU cache and data locality, iterating these collections is much faster than classical object collections.
Objects in a mastodon collection are contiguous in memory.
Mastodon collections have a much smaller memory footprint. It offers an in-memory compact layout storage of objects. Mastodon-collection was developed specifically for this project. Mastodon-collection: a high performance framework to manipulate collections of data. Also, they can be exploited for efficient image processing in special cases, taking advantage of multi-scale pyramidal representation and blocks decomposition. These file formats enable interactive visualization of multi-view TB dataset at the one-time cost of a file conversion. Any file that can be opened in the BDV will work in Mastodon (BDV HDF5 file format, KLB, Keller-Lab Blocks file format, N5 file format. Interactive visualization and navigation of large images thanks to the BigDataViewer ( BDV.
#Manual tracking imagej software#
Mastodon is a Java software that relies on several technologies to achieve these goals, specially developed for it. The tracks are arranged from left to right, and time is laid out from top to bottom. TrackScheme is used to display a hierarchical view of the lineage data. Single objects (spots or links) can be individually edited. Custom tracking algorithms (detection and particle-linking algorithms) ĭisplay image data and overlay the tracking data.Extensible: a 3rd party can build plugins for Mastodon:.Tags and numerical features can then be used to to enrich the visualization. Numerical features and statistics on tracking data.Semi-automatic and fully automatic tracking."Point-wise" interactive editing of the tracking and lineage data.Easily orient the user in a possibly very large annotation. Easy to relate spatial information with hierarchical information. User-friendly framework to navigate through this data.Build tracking and lineage data from images.Interactive browsing, inspection and navigation through the image data.Warning.ĭespite the naming of the artifacts and the apparent usability of the software, Mastodon is still in alpha stage, not released, not published and not supported at the present time. Mastodon is our effort to provide a tool that can harness these challenges. They will make interacting and analyzing the data especially difficult. The challenges of big data are then met twice: first by dealing with a very large image, and second with generating large annotations from this image. However, a single image can amount to several terabytes, and in turn, the automated or semi-automated analysis of these large images can generate a vast amount of annotations. Computational analysis of these images promises new insights in cellular, developmental and stem cells biology. Such images will be 3D over time, possibly multi-channels and multi-view. Modern microscopy technologies such as light sheet microscopy allows live sample in toto 3D imaging with high spatial and temporal resolution. Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
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