Striatum Analysis

Browser adaptation of the Fiji batch macro

Trace the DV, ML, and MV-DL arrows plus three background-noise boxes on each image. The tool extracts line profiles and noise measurements, remembers completed work locally, and exports the same ROI/CSV folder structure used by the original Striatum Analysis Fiji Macro.

1 · Choose a batch

No images selected

Select image files

Or select a folder, including subfolders

Only include filenames containing “MaxIP” Skip TIFF duplicates, matching the Fiji macro

Choose files or a folder. Images remain on this device.

2 · Quantification channel and image settings

ND2 channel to quantify

Channel extraction for PNG/JPEG/BMP/WebP/TIFF

ND2 Z handling

Z slice number (1-based)

Display-only saturated pixels (%)

The 0.35% contrast stretch changes only the screen preview. CSV measurements always use the selected channel’s raw pixel values.

4 · Resume and export

Automatic resume: completed, skipped, and in-progress tracings are stored in this browser. Re-select the same batch after reopening the page to continue. Exporting a project JSON provides an additional portable backup.

Result ZIP: contains ROIs, CSVfiles, processing_log.csv, skipped_images.txt, and project metadata. Each ROI set is an ImageJ-compatible ZIP containing the three arrows and three rectangles. ND2 decoding uses a browser Python/WebAssembly runtime downloaded on first use; images are not uploaded.

Import project JSON