Organella Report
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A figure drawn entirely out of organelles, holding a measuring tape

Organella

measuring label relationships in 2D and 3D

Make a report
pip install organella

organella dry-run experiment/
organella process experiment/ \
    -o report.parquet \
    --object-mask pm --with-mesh

dry-run reads headers only and says what would be measured. --object-mask names the mask that bounds each object, and everything inside it is measured relative to that. --with-mesh adds the geometry the 3D sections draw. Every flag is in the README.

Open one
Drop report.parquet here or click to browse
Your data stays local, nothing is uploaded.
Or load from a URL

Ran with --with-mesh? Once the report is open, press Add geometry and pick either the report_meshes folder or the geometry.parquet files themselves, and the object is drawn in 3D. A browser asks to “upload” a folder you hand it; that is its wording for reading the files, which happens here and goes nowhere.

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Report summary

Do the same structures exist for each ?

In this table, masks and labels per are listed, missing structures are highlighted.

How much of each structure is there?
Looking at a single

Drag to orbit, scroll to zoom, shift-drag to pan. Colour by structure to read the layout, by a metric to see where the extremes sit, or by contact group to see which instances chain together at a given gap. Explode pushes every instance out along its own direction from the centre.

Structure by structure

Every question the report answers about one structure, in one place: how big its instances are, how far they sit from everything else, as labels, as individual pixels of a label, and as label groups by proximity.

Groups of one structure


touching (0)max

Polarity


Radius
The files behind it

What was read, and what was measured of each whole structure.

structurekind instancesextent boundary roundness aspectsizefile