There is something that is not working as before. Probably we tuned to strongly the analyzor for a particular experimental frame. What we did before to find out the proper conditions is to add by hand a selection of our target cells and once characterized we can define better the variables to use in the UMAP and clusters.
1-We generate images of the masks with cell numbers, and select them
2-then in a new column we put a selection = 1, 2, 3 depending on the experiment.
3-we use the selection to see where they appear in the graphics, scatter plots, UMAP, diffmap, etc...
There is something that is not working as before. Probably we tuned to strongly the analyzor for a particular experimental frame. What we did before to find out the proper conditions is to add by hand a selection of our target cells and once characterized we can define better the variables to use in the UMAP and clusters.
1-We generate images of the masks with cell numbers, and select them 2-then in a new column we put a selection = 1, 2, 3 depending on the experiment. 3-we use the selection to see where they appear in the graphics, scatter plots, UMAP, diffmap, etc...