Load Image |
At the prompt, introduce the Z relative resolution for the image. It can be obtained from the file metadata using the default reader or applying the following formula: X (or Y) resolution/Z resolution (all in µm). |
Enter the sequence number (1 - 5) for the channel to be segmented. Using the DNA stain channel for segmentation will detect all cells in the image, however, other channels may be segmented separately too. |
Enter the frame to begin segmentation at (1 by default). Only applies to files with multiple time frames. |
Enhance Image (optional) |
The white and black point of the image can be adjusted to facilitate detection. Generally lowering the white point and re-scaling to 0 - 255 (for 8-bit images) or 0 - 4096 (for 12-bit images) will make the image brighter and facilitate detection of dim nuclei. |
Detect Nuclei |
Select the estimated nuclear diameter (generally between 30 and 40 px in blastocysts). |
For noisy images the noise level can be adjusted. Otherwise, the default value will be applied. |
Segment Nuclei |
Use default parameters. |
Classify Nuclei |
MINS can distinguish trophectoderm (TE) from inner cell mass (ICM) cells in preimplantation embryos based on position. This can also be done manually or based on fluorescence levels if a TE marker is used. |
Export Results |
Select the files to be generated: |
- segmentation overlaid over the channel used (.tiff sequence file), |
- segmentation only (.tiff sequence file), |
- spreadsheet with IDs for all cells detected, XYZ coordinates and fluorescence levels (average and sum) for all channels for each cell (.csv file). |
All files exported by default. Files are saved in the same directory where images are located. |