MedICS Extension: OCT / OCTA Viewer

Interactive viewer for optical coherence tomography (OCT) and OCT angiography (OCTA) volumes, built as a MedICS extension. Use it to load scans, scroll B-scans, generate en-face slabs, overlay layer segmentation, and send volumes back to the MedICS workspace.

Overview

The extension opens a dedicated OCT Analyzer window with a side panel for data I/O and a linked multi-pane viewer:

Pane	What it shows
Left B-scan	Fast-scan (B-scan) OCT, with optional OCTA overlay and layer curves
Right B-scan	Orthogonal (slow-scan / C-scan direction) OCT and OCTA
En-face OCT	Projection of the current slab from the structural volume
En-face OCTA	Projection of the same slab from the flow volume

Crosshairs stay synchronized: moving the indicator on an en-face map updates both B-scans, and moving the mouse on a B-scan reports the matching location on the en-face maps.

Processing stays on your machine. Volumes are never uploaded.

Requirements

• Python 3.11 or later

Installation

pip install medics-ext-oct-viewer

Then start MedICS:

medics
# or
python -m medics

Open OCTViewer from the Extensions menu. The window title is OCT Analyzer.

Supported files

You can load OCT, OCTA, and segmentation independently. Matching pairs are detected by filename suffix (see Paired files).

Role	Typical extensions
OCT (structure)	.foct, .oct, .dcm, .img, .mat, .med
OCTA (flow)	.ssada, .octa, .dcm, .img, .mat, .med
Segmentation	.json, .dcm, .mat, .med (names such as seg.mat, _seg.mat, segmentation.dcm)

Vendor-style names such as cube_z.img / FlowCube_z.img and structural.dcm / flow.dcm are recognized as OCT / OCTA pairs.

A volume is expected as a 3-D array (frames, depth, width). Segmentation is a set of per-B-scan layer curves (see Layer names).

Window layout

The left side panel has three data-source tabs, then frame / transform controls. The slab list sits below the transforms and drives the en-face maps.

1. Workspace — pick arrays already in the MedICS workspace.
2. File — browse or drop files from disk.
3. Transfer — push loaded OCT, OCTA, or segmentation into the workspace under a name you choose.

The status bar (green) shows load progress, mouse coordinates, pixel intensity, and volume shape.

Load data

From the workspace

1. Open the Workspace tab.
2. Choose OCT, OCTA, and/or Segment from the dropdowns. Click the refresh button if you just imported variables in MedICS.
3. The viewer updates as soon as a valid array is selected.

You can also drag a variable from the MedICS variables panel onto the window (ws.variable_name). Volumes load as OCT/OCTA; curve dictionaries load as segmentation (you will be asked to confirm).

From files

1. Open the File tab.
2. Click the folder button next to OCT, OCTA, or Segment, or type / drop a path into the corresponding field.
3. Uncheck the OCTA checkbox if you only want structural OCT.
4. Click Load Data.

You can drop a file onto a path field, onto Load Data, or onto the window:

• Known OCT / OCTA / segmentation suffixes load immediately.
• A .mat or .med file that contains several arrays opens a picker so you can assign OCT, OCTA, and Segment keys.
• Any other suffix asks whether to treat the file as OCT, OCTA, or segmentation.

Custom readers

Click setting... on the File tab to point at a Python file or folder of loader functions. Assign a function to OCT, OCTA, and/or segmentation, or leave default to use the built-in readers. This is useful for proprietary or lab-specific formats.

Paired files

When you load an OCT file, a sibling OCTA file with the paired suffix is looked up automatically (for example .foct ↔ .ssada, oct.dcm ↔ octa.dcm). The same idea applies to segmentation files named *seg.mat, *_seg.mat, *segmentation.dcm, and similar.

Navigate the volume

Frame control

• Frame spin box: current B-scan index (1-based in the UI).
• Up / Down (while a viewer pane is focused): previous / next B-scan.
• Left / Right: jump 10 B-scans at a time.

Linked crosshairs

• Click or drag the crosshair on an en-face map to choose the B-scan (horizontal line) and A-scan (vertical line).
• Move the mouse over a B-scan to see the matching point on both en-face maps and the intensity in the status bar.

Zoom and pan

Standard image-viewer gestures apply in each pane (scroll to zoom, drag to pan). Use transpose on an en-face map if the fast/slow axes look swapped.

Hide panes

Use the collapse buttons next to the en-face OCT and OCTA maps to hide one projection and give more space to the other. B-scan docks can be resized by dragging the splitters.

En-face slabs

En-face images are projections of all voxels between an upper and lower boundary. Pick a preset on the slab panel, or edit the custom formula.

Presets

Group	Slabs
Regions	Vitreous, Retina, Inner, Outer, Choroid
Vascular (OCTA)	SVC, DVC, NFLP, GCLP, ICP, DCP
Layers	NFL, GCIPL, INL, OPL, ONL, EZ, IZ, RPE
Choroid	CC, Sattler, Haller

Retina (ILM → EZ) is selected by default.

Each preset is a linear combination of two layer surfaces plus a pixel offset, for example:

upper = 1.0 × ILM + 0.0 × ILM + 0
lower = 1.0 × EZ  + 0.0 × ILM + 0

You can mix two layers (ratios need not sum to 1) and shift the surface in depth with the + offset spin boxes. Changes update both en-face maps and the slab overlay on the B-scans.

Projection mode

For each en-face map independently:

Mode	Meaning
Mean	Average intensity in the slab (default for OCT)
Maximum	Maximum intensity (default for OCTA)
Minimum	Minimum intensity
Thickness	Slab thickness in pixels (no volume required)

Contrast and colormap

Each pane has a color bar and low/high spin boxes. Click the color bar to choose a colormap (grayscale for OCT, hot-style for OCTA by default). Adjust the range to brighten faint vessels or compress bright vitreous.

Layer overlay

If segmentation is loaded, the named curves are drawn on both B-scans. The same surfaces define slab boundaries for en-face projection.

Layer names

#	Name	Typical anatomy
1	PVD	Posterior vitreous detachment
2	ILM	Inner limiting membrane
3	NFLGCL	NFL / GCL
4	GCLIPL	GCL / IPL
5	IPLINL	IPL / INL
6	INLOPL	INL / OPL
7	OPLONL	OPL / ONL
8	ELM	External limiting membrane
9	EZ	Ellipsoid zone
10	EZIZ	EZ / IZ
11	IZRPE	IZ / RPE
12	RPEBM	RPE / Bruch’s membrane
13	SATHAL	Sattler / Haller
14	CHOROID	Choroid outer boundary

If no segmentation file is provided, empty curves are created so you can still use depth ROI and (limited) slab controls. Flattening to RPE-BM needs a valid RPEBM surface.

Layer segmentation itself is a separate extension (medics-ext-retinal-layer-segmentation); this viewer displays and uses those results.

Transforms

The Data Transform group applies to the currently loaded volumes.

Control	What it does
Flatten	None, Fitting, or RPE-BM. Fitting / RPE-BM axially flatten the retina (and OCTA, if loaded) so en-face slabs follow anatomy. RPE-BM uses the RPEBM curve.
Permute	Reorder axes (0,1,2 is frames, depth, width). Use this when a vendor volume is stored in a different order.
Flip Axis	None, Left-Right, or Up-Down.
ROI	Top and bottom depth indices. Auto estimates a retina-containing band so projections ignore empty vitreous/sclera.

Flattening can take a few seconds on large volumes; a progress dialog is shown. Segmentation curves are updated to stay aligned with the flattened data.

Scan resolution

Click Update data resolution to set:

• scan width and height in millimetres
• axial (depth) sampling in millimetres per pixel

Lateral pixel size is computed from scan size ÷ number of A-scans / B-scans. Axial resolution is a device specification — use the help button in the dialog if you are unsure. Correct millimetre scaling matters if you later quantify thickness or export to other MedICS tools.

Send data to the workspace

On the Transfer tab:

1. Optionally rename the variables (oct_data, octa_data, seg_data by default). Names must be valid Python identifiers.
2. Click >> next to OCT, OCTA, or Segment.

The arrays appear in the MedICS workspace and in the Workspace dropdowns after refresh. Use this to hand volumes to other extensions (layer segmentation, quantification, custom scripts).

Typical workflows

Review a paired OCT / OCTA cube

1. Drop the .foct (or .oct / DICOM) file onto Load Data.
2. Confirm OCTA was auto-filled (.ssada / .octa / flow.dcm).
3. Click Load Data.
4. Scroll B-scans with Up/Down. Click the en-face map to jump to a region of interest.
5. Select SVC or DVC and set OCTA projection to Maximum.

Inspect a segmented retina

1. Load OCT (and OCTA if available).
2. Load the matching *_seg.mat / .json / .med segmentation.
3. Confirm layer curves overlay the B-scans.
4. Choose Retina, NFL, or a custom ILM–RPEBM slab and switch projection to Thickness for a thickness map.

Flatten for cleaner en-face maps

1. Load OCT and a segmentation that includes RPEBM.
2. Set Flatten to RPE-BM (or Fitting).
3. Re-select the slab. Choroid and outer-retina projections usually look more uniform after flattening.

Work from the MedICS workspace

1. Import or compute volumes in MedICS (Import Data, Jupyter, another extension).
2. Open OCTViewer → Workspace and pick the arrays.
3. After review, use Transfer to write a copy under a new name.

Tips

• Uncheck OCTA before Load Data if the paired flow file is missing or you only need structure.
• If B-scans look rotated or the en-face map is stretched, try Permute and transpose on the en-face pane before assuming the file is wrong.
• Auto ROI is a good first step when vitreous or deep choroid dominates the projection.
• Drop .med / .mat containers rather than guessing keys — the group picker lists every array in the file.
• The status bar reports shape as frames × depth × width after load.

Troubleshooting

Problem	What to try
Load Data says invalid path	At least one of OCT / OCTA / Segment must be a real file. Empty fields are fine; typo paths are not.
OCTA did not appear	Check the OCTA checkbox, confirm the paired suffix, or browse the flow file manually.
En-face is blank / noise	Load or create segmentation, pick a slab that sits on the retina, or run Auto ROI. Flattening often helps.
Layers do not match B-scans	Check Permute and Flip. Segmentation stores its own permute/flip and is reapplied when you change those controls.
Flatten does nothing useful	RPE-BM needs a valid RPEBM curve. Use Fitting if you only have OCT.
Axes look swapped on en-face	Use the transpose button on that en-face map.
Custom format will not load	Use setting... and point at a Python function that returns a 3-D NumPy array (or a curve dict for segmentation).
Extension does not show in the menu	Confirm pip show medics-ext-oct-viewer in the same environment as MedICS, then restart MedICS.

Links

• Homepage: Medical-Image-Computing-Suite.github.io
• Documentation: Community wiki
• Issues: Community issues
• Package: medics-ext-oct-viewer on PyPI

License

Proprietary. Contact medics.support@gmail.com.