Opening and Creating a Series

Opening and Creating a Series

On first launch

With no file specified, PyReconstruct opens a welcome series — a small, read-only demo you can use to explore the interface. The welcome series cannot be saved or backed up; create or open a real series to begin work. A username is resolved automatically and recorded against the edits you make — PyReconstruct no longer prompts for it on launch; change it anytime under File ▸ Change username….

Opening an existing series

File ▸ Open (Ctrl+O) opens a .jser file. Recently opened series are listed under File ▸ Open recent. File ▸ Close returns to the welcome series (it does not quit the app).

If a series' image files can't be found when it opens, PyReconstruct asks whether you'd like to locate them and lets you pick the image folder (you can also do this later via Series ▸ Images ▸ Find/change image directory).

Recovering an unsaved session. If a series was left open or not saved cleanly (for example after a crash), reopening it detects the leftover working folder and offers to recover the unsaved session. If the same series appears to be open in another window (it was touched within the last few seconds), PyReconstruct shows "Series In Use" and declines to open a second copy.

Creating a new series from images

File ▸ New ▸ From images… (Ctrl+N) walks you through:

1. Select images — choose the section image files (JPG/JPEG, PNG, TIF/TIFF, BMP). The files are sorted alphanumerically, and that order becomes the section order (section 0, 1, 2, …), so name your images so they sort correctly.
2. Series name — used to name the series.
3. Image calibration (µm/px) — microns per image pixel. Default 0.00254.
4. Section thickness (µm) — default 0.05. Thickness feeds the volume and flat-area calculations in the object list.

The new series opens fitted to the first image; you are then prompted to choose where to save the .jser.

📸 Screenshot: the New Series calibration / thickness prompt.

Other ways to create a series

Also under File ▸ New:

• From scaled images… — build from an existing scaled Zarr directory (expects a scale_1 folder), then the same name/calibration/thickness prompts.
• From legacy .ser… — create from legacy Reconstruct XML .ser files.
• From neuroglancer zarr… — create from a Neuroglancer Zarr.

Image directory and Zarr conversion

Under Series ▸ Images:

• Find/change image directory — point the series at the folder containing its images. The chosen directory is remembered with the series.
• Convert to scaled images — convert the series' images into a scaled (.zarr) store for faster loading of large images.
• Update image scales — add or refresh scale levels on an existing Zarr.

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