tiff to omezarr and nrrd to precomputed converters

converters/dm3_to_omezarr/README.md

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+# DM3 to OME-Zarr Converter
+
+This converter stitches 9 DM3 tile montages into a single OME-Zarr volume.
+
+## Tile Organization
+
+The input data consists of 9 montage folders (Montage_000 to Montage_008) arranged in a 3x3 grid:
+
+```
+Row 1 (top):    Montage_006 | Montage_007 | Montage_008
+Row 2 (middle): Montage_003 | Montage_004 | Montage_005
+Row 3 (bottom): Montage_000 | Montage_001 | Montage_002
+```
+
+Each montage folder contains .dm3 files numbered sequentially, representing z-axis slices.
+
+## Installation
+
+Install the required dependencies:
+
+```bash
+pip install -r requirements.txt
+```
+
+## Usage
+
+### Basic Usage
+
+```bash
+python converter.py <input_folder> <output_zarr>
+```
+
+Example:
+```bash
+python converter.py ./data ./output.zarr
+```
+
+### Custom Chunk Size
+
+You can specify custom chunk sizes for the Zarr storage:
+
+```bash
+python converter.py ./data ./output.zarr --chunk-size 1 1024 1024
+```
+
+The chunk size is specified as Z Y X dimensions.
+
+## Input Structure
+
+Your input folder should have the following structure:
+
+```
+input_folder/
+├── Montage_000/
+│   ├── 0.dm3
+│   ├── 1.dm3
+│   ├── 2.dm3
+│   └── ...
+├── Montage_001/
+│   ├── 0.dm3
+│   ├── 1.dm3
+│   └── ...
+├── Montage_002/
+│   └── ...
+├── Montage_003/
+│   └── ...
+├── Montage_004/
+│   └── ...
+├── Montage_005/
+│   └── ...
+├── Montage_006/
+│   └── ...
+├── Montage_007/
+│   └── ...
+└── Montage_008/
+    └── ...
+```
+
+## Output Format
+
+The output is an OME-Zarr file following the OME-Zarr 0.4 specification with:
+- 3D volume (Z, Y, X)
+- Compressed using Blosc/zstd
+- Multiscale metadata for visualization
+- Spatial coordinate system
+
+## Features
+
+- **Automatic stitching**: Tiles are automatically stitched in the correct spatial arrangement
+- **Progress tracking**: Real-time progress bars for conversion
+- **Error handling**: Robust error handling for missing files or montages
+- **Efficient storage**: Chunked Zarr format with compression
+- **OME-Zarr compatible**: Can be visualized with Neuroglancer, napari, and other OME-Zarr viewers
+
+## Troubleshooting
+
+### Missing montage folders
+If some montage folders are missing, the converter will log warnings and leave those regions empty (zeros).
+
+### Different tile sizes
+All tiles are expected to have the same dimensions. If tiles have different sizes, adjust the code accordingly.
+
+### Memory usage
+The converter processes one z-slice at a time to minimize memory usage. Adjust chunk sizes if you encounter memory issues.