When you select the ROIs yourself outside of the plugin and then select the "ROI Manager" as the cell identification input the plugin cannot work properly. In the Cell Filter preview it only selects the gaps between the cells but none of the cells itself.
If you then try to proceed regardless of this issue you get the following error message in FIJI:
**Warnings**
(ezcol.cell.CellDataProcessor.mask2data(CellDataProcessor.java:84)): No cell is found based on the selected filters on some slices.
Apply ROIs to all slices in Settings->Parameters->Apply ROIs to all slices.
(ezcol.main.AnalysisOperator.applyToStack(AnalysisOperator.java:421)): No cell can be found in cell data processor on slice 1
Did someone perhaps experience a similar problem? My strategy is the following: I use my brightfield cell image for the identification, here I am using CellPose to identify my cells and create a binary image. This binary image I am then watershedding and transform this into a mask. This mask I am analyzing using the analyze particile function and add the ROIs to my overlay.
When you select the ROIs yourself outside of the plugin and then select the "ROI Manager" as the cell identification input the plugin cannot work properly. In the Cell Filter preview it only selects the gaps between the cells but none of the cells itself.
If you then try to proceed regardless of this issue you get the following error message in FIJI:
**Warnings** (ezcol.cell.CellDataProcessor.mask2data(CellDataProcessor.java:84)): No cell is found based on the selected filters on some slices. Apply ROIs to all slices in Settings->Parameters->Apply ROIs to all slices. (ezcol.main.AnalysisOperator.applyToStack(AnalysisOperator.java:421)): No cell can be found in cell data processor on slice 1
Did someone perhaps experience a similar problem? My strategy is the following: I use my brightfield cell image for the identification, here I am using CellPose to identify my cells and create a binary image. This binary image I am then watershedding and transform this into a mask. This mask I am analyzing using the analyze particile function and add the ROIs to my overlay.