AlignRef2 — Web beta

1 Load images

JPG / JPEG / PNG / TIFF · natural filename order

Your images stay on your device. Images you load are processed locally in your browser and are not uploaded to any server.

Mouse brain Nissl serial sections
132 images · 1080 × 840 · subj03

Demo data info

Every other section retained. Demo data: Mouse Brain Architecture Project (BAP).

Images: CC BY-SA 4.0, under the BAP Policy. Source host: JHU subj03 distribution.

Prepared for this demo: odd-numbered sections only, common canvas, JPEG. Data license & attribution. AlignRef2 code is separately Apache-2.0. No BAP or JHU endorsement is implied.

Downloads about 9.84 MB only when you click. Choose images or a folder again to replace the demo stack.

Canvas background

TIFF support & bit depth

Single-page, strip-based unsigned 8/16-bit grayscale or RGB TIFF; uncompressed, LZW or Deflate. Top-left orientation, interleaved samples, no alpha.

16-bit samples map from 0–65535 to 0–255. Display, registration and PNG/JPEG export are 8-bit; the original TIFF file is preserved. There is no automatic contrast stretch.

Multi-page, tiled, BigTIFF, signed/float, palette/CMYK, alpha, PackBits/JPEG/CCITT and other orientations are not supported. The TIFF decoder is bundled locally; no runtime CDN.

Original pixels preserved. Smaller images are center-padded.

2 Automatic registration

ChannelProxy limit

Reference

Translation + rotation only. Pairwise alignment outward from the reference. Review every slice.

Local registration engine ready.

Registration warnings

No registration run for this stack.

3 Manual refinement

Overlay opacity

Flicker

No correction recorded

W A S D move 1 px · Q E rotate 0.1°
Shift ×10 · active while recording

Position range Start: — End: —

Apply range: set Start and End.

4 Crop

Drag a rectangle in the viewer. Drag inside to move; drag corners to resize.

XYWidthHeight

5 Export

FormatJPEG quality

Transforms map by natural slice order; count and each source size must match. ZIP is limited to 256 MB of encoded files.

No stack loaded—

Start with your serial images

Choose a folder or multiple images in step 1.
Align, inspect and refine — entirely in your browser.

01 LOAD → 02 REGISTER → 03 REFINE → 04 CROP → 05 EXPORT

Rigid transform: —QC: —

Ready. Chrome / Edge desktop recommended.

Keyboard shortcuts & beta limits

Outside recording: ←/→, R/F, U/J, PageUp/PageDown navigate. During recording: WASD, OKL;, arrows translate; Q/I and E/P rotate. Shift gives 10 px / 1°. Over the viewer, wheel up/down selects the previous/next slice (one step per burst; pause 180 ms between bursts). Ctrl+wheel zooms. Wheel navigation pauses while recording, processing or editing a form field. Drag the viewer to pan outside crop mode. Finish stores a correction only; Apply changes the selected range once.

Designed for adjacent slices with similar content, roughly ±30° rotation and moderate displacement. Low-texture, repetitive, damaged or substantially different slices may fail. QC correlation is an image similarity indicator, not a scientific accuracy estimate. No DICOM, 16-bit export/preservation, scale or deformation in this beta. See step 1 for the supported TIFF subset. Save transforms before closing or loading another stack.