Mark Keller

Support sphere-based selection of entities in 3D

1

**User story** ParaGlyder: Probe-driven Interactive Visual Analysis for Multiparametric Medical Imaging Data https://link.springer.com/chapter/10.1007/978-3-030-61864-3_29 **Preferred solution** **Possible alternatives**

**User story** If we embrace Arrow+DuckDB internally for data representation, it will open the possibility to offload the DuckDB to a different process, for example in Python. In that case,...

**User story** See discussion on slack for more context https://hms-dbmi.slack.com/archives/GU9AJC1Q8/p1679861686708629 **Preferred solution** > This could either be done before passing to Vitessce `` or we could implement a new feature...

**To Reproduce** Steps to reproduce the behavior: https://portal.hubmapconsortium.org/preview/multimodal-mass-spectrometry-imaging-data use dropdown to switch from initial config to another config **Expected behavior** A clear and concise description of what you expected to...

**User story** User feedback: > In Vitessce's spatial visualization module, there's a limitation when rendering multi-channel data. Specifically, when visualizing datasets with high dimensionality of channels using both the spatial...

**User story** User does not have a per-observation centroid (x,y) coordiante OR in 3D case, it is complicated to store (x,y) coordinates for each Z slice per-observation. Also, even when...

**User story** Currently data loading in the config is not very reactive as the current data hook function dependencies only take into account dataset IDs which effectively prevents data reloading...

spatialBeta segmentationLayer->segmentationChannel user-defined set selections are not colored as expected when no dataset-defined sets exist

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**User story** For some reason, in `spatialBeta` view, segmented observations (at least with polygons) currently only take on the colors of lasso-selected obsSets when there are also dataset-defined `obsSets`. For...

Load bitmasks stored in OME-XML

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**User story** GeoMx outputs store the "segments" in binary fields within the OME-XML **Preferred solution** Add a fileType for `obsSegmentations.ome-tiff-xml` (as opposed to `obsSegmentations.ome-xml` which in theory could also be...

**User story** User defines a grid with views that do not have a min/max coordinate of `[0, 12]`. Vitessce tries to auto-rescale the min/max of the grid to something nice....