I'm a a bit confused by your description as to what you're seeing that is making it difficult to sort cells. Perhaps a screenshot of CPA would be helpful? Or a screenshot of the types of objects you are trying to classify?
In any case, there are a couple of tips to help with visually making things out:
- For each tile shown in Classifier, there is a small square that appears in the middle of the tile. Whatever cell/object is under the tile is the one that is being classified. This is the case even if another object is visible off to the side of the tile.
- If sorting cells, we typically set the object to be centered in the tile as the nuclei (rather than the cell or something else) since the nuclei are usually easy to make out and are well separated.
- In CPA, you can adjust the color contrast of the tile by selecting View > Image Controls
from the Classifer menu, and changing the "Contrast Stretch". - Finally, you can add outlines to the list of images to display in CPA by saving them using SaveImages by set "Record file and path information..." to "yes". In CPA, the outlines will then show up in the tiles as well.