Exporting microscope images for analysis
What microscope software shows on screen is adjusted to look good. Quantitative analysis needs a file that holds the original, unadjusted values.
Try it with the tool
Upload per-channel TIFFs (_ch00, _c1, _DAPI) together and they are merged automatically; 16-bit, OME-TIFF and z-stacks (MIP) are supported.
Open the FISH tool →1. Always keep the original
Vendor formats — .czi (Zeiss), .lif (Leica), .nd2 (Nikon) — hold every channel, the bit depth, pixel size and acquisition settings. Keep them even after exporting TIFFs; you will need them for review or re-analysis.
2. Good export formats for analysis
- One grayscale TIFF per channel, with the channel in the file name (_ch00, _c1, _DAPI).
- Keep the original bit depth (12/16-bit); reducing to 8-bit loses faint-signal resolution.
- OME-TIFF: a standard format that holds several channels and metadata in one file.
- Merged RGB images are for presentation; per-channel files are more accurate for analysis.
3. In Zeiss ZEN and Leica LAS X
Menu names vary slightly between versions.
- Zeiss ZEN: File → Export (or the Image Export / Batch tools under Processing) → TIFF; choose separate channels and the original bit depth, and turn off annotations and scale bars.
- Leica LAS X: right-click the image → Export → TIFF; choose per-channel (grayscale) and raw data, and turn off overlays.
4. Common pitfalls
- Display adjustments saved: exporting “as displayed” after boosting brightness destroys the original values.
- Burned-in annotations: arrows, text and scale bars become pixels and contaminate analysis.
- JPEG: compression smears small spot signals.
- Z-stacks: a single plane misses signals in other planes; a maximum-intensity projection (MIP) is standard.
Upload per-channel TIFFs (_ch00, _c1, _DAPI) together and they are merged automatically; 16-bit, OME-TIFF and z-stacks (MIP) are supported.
Open the FISH tool →