Are these 10x samples too low quality for downstream analysis?

Question

[AHerik]

Hello! I'm running some samples for a collaborator. They sequenced small intestine cells post-infection, and even prior to sequencing the cells were quite apoptotic. 10k cells were loaded per sample, and per sample only 3k, 4k, and 5k cells were recovered.

I'm trying to figure out the QC cutoffs for the samples now, as the collaborator would like to move forward with the given samples. I see a lot cells with high MT content, but "okay" feature and gene expression.

Any suggestions on how stringent I should be with the filtering? Does it also make more sense to do it on a sample by sample basis? Or is this data unusable?

Thanks!