OCT E2E Viewer

A small desktop app for scrolling through the B-scans of a Heidelberg Heyex .E2E OCT file, one slice at a time, with the current slice's position marked on the en-face fundus image. It can also open a plain directory of B-scan PNGs when you don't have the original .E2E file. Built on eyepy for reading .E2E files and Qt (PySide6) for the UI.

Install

The easiest way to install is with pipx, which puts the app in its own isolated environment and puts the oct-e2e-viewer command on your PATH, without you needing to create or activate anything:

pipx install git+https://github.com/MakrisJr/oct-e2e-viewer.git

(Install pipx itself first if you don't have it: python3 -m pip install --user pipx && python3 -m pipx ensurepath.)

If you're developing on the code instead, use an editable install in a venv (or conda env) of your own:

python3 -m venv .venv
source .venv/bin/activate
pip install -e .

Either way, this installs the oct-e2e-viewer command and the oct_e2e_viewer package, including PySide6, so no system Qt/GUI packages need to be installed separately.

Note: editable installs (pip install -e . or pipx install --editable .) don't re-resolve dependencies on their own. If you pull changes that add or update a dependency and the app then fails to start with an import error, re-run the install command to pick up the change.

Run

oct-e2e-viewer                     # opens with File > Open
oct-e2e-viewer path/to/scan.e2e    # opens a .E2E file directly
oct-e2e-viewer path/to/png_dir     # opens a directory of B-scan PNGs directly

You can also drag and drop a .e2e/.E2E file or a directory of PNGs onto the window, or use File > Open File... / File > Open Directory... (Ctrl+O / Ctrl+Shift+O).

Opening a directory of PNG B-scans

If you have B-scans exported as individual images, point the app at the folder they're in (File > Open Directory..., Ctrl+Shift+O, drag-and-drop, or oct-e2e-viewer path/to/dir on the command line):

• Every .png file directly inside that folder is loaded as one B-scan slice (subfolders aren't searched).
• Files are ordered by the numbers in their filename, not alphabetically (so scan-2.png sorts before scan-10.png regardless of digit padding), and file names don't need to follow any particular convention (004-0.png, bscan_07.png, 12.png all work) as long as the slice order is encoded somewhere in the number(s) in the name.
• Each image is converted to 8-bit grayscale on load, whatever its original color mode.

A directory laid out like this works out of the box:

004/
    004-0.png
    004-1.png
    004-2.png
    ...
    004-48.png

Because a plain PNG folder carries none of an .E2E file's extra data, a few things are unavailable and the UI adapts accordingly:

• No fundus/localizer image — the app shows just the B-scan (no empty "No fundus image" panel).
• No laterality, scan date, quality, averaging, or axial-scale metadata in the status bar.
• No layer segmentations — the "Layer annotations"/"Layer Legend" controls and B-scan alignment (which needs a segmented reference layer) have nothing to draw.

Controls

Navigation

• Left/Right arrow keys, mouse scroll wheel (over the chart), the slider, the index box, or Prev/Next buttons: step through B-scans.
• Page Up/Page Down: jump 10 slices at a time.
• Home/End: jump to the first/last B-scan.
• Type an index in the box and press Enter to jump directly to it.

Setup double-click to open (Linux)

To make this app the default handler for a .e2e/.E2E file, run this after the installation:

oct-e2e-viewer --install-desktop-entry

It registers a MIME type for .e2e/.E2E files, installs a .desktop launcher (with icon) under ~/.local/share/applications, and sets it as the default handler via xdg-mime. It's a user-level install (no sudo).

Project layout

src/oct_e2e_viewer/
    loader.py                # thin wrapper around eyepy's import_heyex_e2e
    png_loader.py            # loads a directory of B-scan PNGs
    app.py                   # PySide6 (Qt) UI
    alignment.py             # B-scan alignment ("Stabilize B-scan Position")
    recent_files.py          # Open Recent persistence
    desktop_integration.py   # `--install-desktop-entry` (Linux launcher + MIME type)
    resources/               # icon, .desktop template, MIME type definition