Hello CellProfiler Team and all the community members,
Following the release of CP4, we considered to migrate from CP3 to CP4, especially to benefit of the performance improvement.
For this, we migrated our main pipeline to be CP4 compatible, and run a test on 2 different datasets.
To make it compatible, we had to remove the LoadImage module which is deprecated and use Image, Metadata, … instead.
We focus our verification on the existing CP3 metrics.
The tests have been done with the same images and the same input values.
As a result:
For the masks:
the main part was very similar or equal for CP3 / CP4 runs.
Some of them have significant difference (such as merging 2 cells into 1), but this may be potentially resolved by finetuning of thresholding settings (to be checked).
For the metrics:
- Even by focusing on the “very similar or equal” images, we can see that results are similar… modulo a multiplying factor. For instance:
|DataSet1 (6 images)||Dataset2 (2 images)|
|Mutliplying Fact.||Mutliplying Fact.|
Looks like the impacted metrics are the ones linked to “MeasureObjectSizeShape”
Did someone observe same behavior and/or have any explanation about these multiplying factors?
For the compactness for dataset1, the values for dataset 1 were around 30 with CP3, and now around 2… Any idea about which values looks relevant?