If you want to analyse something you have to have an adequate theoretical background a practical experiences. This idea has to be applied to all instruments, not only SEM and TEM. Now you need a lot of time and patience for reading relevant books.
The best way is by taking a course on SEM and a course on TEM with access to SEM & TEM facilities in a university. Also, you can take a short course on SEM as well as on TEM with access to SEM & TEM facilities in a conference meeting like SCANNING annual meeting, MMC meeting, and so on.
The courses will provide not only a theoretical background but also, hands-on experience on SEM&TEM analysis.
For the images obtained from biological samples in TEM, the automatic analyzers do not work because the automatic analysis does not differentiate between the gray level of a mitochondrion and a nucleus for example ... The human eye is the only one able to distinguish between the different structures that It has a cell.
Another thing is if you want to count particles, which stand out strongly on the background in each image obtained the TEM
I think that more interesting than seeing literature is learning to analyze images together with an expert. This is what is done in medicine for diagnostic imaging.