Core Concepts

Core Concepts

PyReconstruct is organized around serial-section microscopy: a block of tissue is cut into an ordered stack of thin sections, each imaged, and structures are traced through the stack.

• Series — a complete project: an ordered set of sections plus series-wide settings. You work on one series at a time. A series is stored as a single .jser file (see below).
• Section — one cross-section in the stack. Each section has an index, a background image, a magnification (mag, in µm per image pixel), a thickness (in µm), brightness/contrast, and its own set of traces.
• Trace — a single connected shape or curve drawn on one section. A trace can be closed (an outline enclosing area, e.g. a cell cross-section) or open (a curve with length but no enclosed area, e.g. a process or a measurement line).
• Contour — all traces with the same name on a single section.
• Object — all traces with the same name throughout the whole series. Objects are what you reconstruct in 3D and measure in the object list.
• Z-trace — a single curve that runs across sections (its points carry a section index), used to measure distances through the volume.
• Flag — a labeled, optionally colored marker placed at a point on a section, with comments and a resolved/unresolved state. Flags are useful for to-do notes, questions, and review.
• Transform — a section's affine transform, six numbers a b c d e f: a b d e give rotation/shear/scale and c f give x/y translation. The same transform is applied to the section's image and its traces, so traces stay fixed to the image — moving the alignment moves image and traces together.
• Alignment — a named set of per-section transforms across the whole series. A series can hold several alignments and you can switch between them. (See Alignment.)
• Host / traveler — an optional parent/child relationship between objects: an object can be hosted by ("ride on") another object. Used to keep related structures organized and to group them in the 3D scene.

The .jser file

A series is saved as a single .jser file. It is a JSON document with the series-level settings, the per-section data (including each section's image filename, magnification, and thickness), and the edit log. The .jser does not contain the images themselves — it stores image filenames, and the actual image files live in the series' image source directory. While a series is open, PyReconstruct unpacks it into a hidden working folder next to the .jser and repacks on save.

Images and Zarr

Supported image formats for sections are JPG/JPEG, PNG, TIF/TIFF, and BMP.

For large images, PyReconstruct can use multiscale Zarr image stores, which load only the parts of the image needed for the current view (rather than the whole image on every section change). You can convert a series' images to scaled Zarr from Series ▸ Images ▸ Convert to scaled images (see Opening and creating a series).

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