Preprocessing Module

Prepare a grayscale image stack for the rest of the pipeline: crop it, trim its slice range, flip or rotate it, downscale it, adjust its intensity, and convert its bit depth. Every operation is optional.

The Preprocessing module reads a single image stack, lets you configure a set of operations while previewing intensity changes on the current slice, and writes the result as a new workspace file. The original stack is never modified.

Key Features

• Non-destructive: the result is saved as a new tracked file; the input is left untouched

• Fixed, predictable operation order so results are reproducible

• Live intensity preview on the current slice, with a crop rectangle drawn as an overlay

• Lineage tracking that links the output back to the input, including the crop origin

• Voxel size inherited from the input and rescaled when you downscale

Operation Order

Operations always run in the same fixed order, regardless of the order you set them in the interface:

1. Crop (xy rectangle, in original coordinates)

2. Z-range trim (keep a contiguous slice range)

3. Flip (horizontal, then vertical)

4. Rotate (90 / 180 / 270 degrees)

5. Downscale (mean binning)

6. Intensity (window / gamma / invert)

7. Data-type conversion (output bit depth)

Lineage and Voxel Size

• The output file records a lineage entry linking it to the input file.

• When a crop or z-range is applied, the crop origin (x, y, z) is stored on the lineage. The stitching module uses this to prefill its recipe.

• Voxel size is carried over from the input. When you downscale, the xy voxel size is multiplied by the downscale factor.

Workflow

1. Select Stack: Pick a grayscale stack (raw upload or processing result)

2. Adjust: Configure crop, z-range, geometry, intensity, and output type

3. Apply: Review the summary and write the preprocessed stack as a new file