There have been many issues that have come from the second plate with the NF1 data.
But the main issue at the current moment, when we have received all images that are .tif
files, they came as RGB (3 channel) images and contained a scale.
When we received the updated second plate dataset, the images were still RGB but did not contain the scale.
What I noticed is that when splitting the images in CellProfiler to take the one channel connected to the colored channel in a composite Cell Painting image, there were discrepancies in how CellProfiler displayed the split channels.
Here is what it looks like with the images with scale:
![image](https://user-images.githubusercontent.com/107513215/207159343-c815093c-ef3a-44a7-8391-8b65d46d5690.png)
Here is what is looks like with the updated images without the scale:
![image](https://user-images.githubusercontent.com/107513215/207640266-c3f49fec-01c5-4521-b56e-5a70b4130f52.png)
As seen in both images, the OrigGreen
channel in the scaled image is less intense compared to in the non-scaled image, where OrigGreen
and GrayBlue
look like the exact same image.
I am unsure of if this makes a difference in terms of image quality. I am only taking one channel from the split RGB images so what I expect could happen is loss of some data but maybe not. These are my observations of the current discrepancies between NF1 datasets.