Data requirements
Before uploading, each slice should include a complete image set that supports registration, cell detection, and downstream analysis.
Required image set per slice
For each slice, prepare:
- DAPI 4x: Required for atlas registration
- DAPI 20x: Required for cell detection and 20x-to-4x alignment
- 20x for each non-DAPI staining: Required for marker-specific analysis
Example:
If your project has DAPI, c-Fos, and NeuN, each slice should have:
- DAPI 4x
- DAPI 20x
- c-Fos 20x
- NeuN 20x
Why each image is needed
DAPI 4x
Used for atlas registration (DeepSlice) to place the slice in anatomical context.
DAPI 20x
Used for automated cell detection (StarDist) and as the high-resolution reference channel.
20x non-DAPI channels
Used to classify and quantify signal-positive cells per staining channel.
What happens if images are missing
- Missing DAPI 4x: Atlas registration cannot run
- Missing DAPI 20x: Cell detection cannot run
- Missing 20x non-DAPI for a configured staining: That channel cannot be analyzed for that slice
Supported formats
Upload supports standard microscopy image formats:
- TIFF (
.tif,.tiff) - PNG (
.png) - JPEG (
.jpg,.jpeg)
Imaging best practices
Use consistent acquisition settings across animals and conditions.
- Exposure: Keep exposure and gain consistent within a channel
- Focus: Ensure sharp focus before batch acquisition
- Dynamic range: Avoid clipping saturated regions
- Channel naming: Keep staining labels consistent with your Study setup
- Scale/magnification: Verify 4x and 20x labels are correct in exported filenames
Small acquisition inconsistencies are manageable, but strong variability can reduce comparability across slices and groups.