dynamic optical transmission (dot). three primary fluorophores are able to generate a total of 7 readily detectable emission spectra as a result of combinatorial labeling using dot. hybrid fusion fish enables highly multiplexed fish applications that are targeted within clinical oncology panels. the technology offers faster scoring with efficient probesets that can be readily detected with traditional fluorescent microscopes. merfish multiplexed error-robust fluorescence in situ hybridization is a highly multiplexed version of smfish. it uses combinatorial labeling, followed by imaging, and then error-resistant encoding to capture a high number of rna molecules and spatial localization within the cell. the capture of a large number of rna molecules enables elucidation of gene regulatory networks, prediction of function of unannotated genes, and identification of rna molecule distribution patterns, which correlate with their associated proteins. starfish starfish is a set of software tools developed in 2019 by a consortium of scientists to analyze data from nine different variations of fish, since all variations produce the same set of data—gene expression values mapped to x and y coordinates in a cell. the software, created for all scientists, not just bioinformaticians, reads a set of images, removes noise, and identifies rna molecules. this approach has set out to define a standard analysis scheme of fish datasets in a similar way to single-cell transcriptomics analysis. medical applications often parents of children with a developmental disability want to know more about their child's conditions before choosing to have another child. these concerns can be addressed by analysis of the parents' and child's dna. in cases where the child's developmental disability is not understood, the cause of it can potentially be determined using fish and cytogenetic techniques. examples of diseases that are diagnosed using fish include prader-willi syndrome, angelman syndrome, 22q13 deletion syndrome, chronic myelogenous leukemia, acute lymphoblastic leukemia, cri-du-chat, velocardiofacial syndrome, and down syndrome. fish on sperm cells is indicated for men with an abnormal somatic or meiotic karyotype as well as those with oligozoospermia, since approximately 50% of oligozoospermic men have an increased rate of sperm chromosome abnormalities. the analysis of chromosomes 21, x, and y is enough to identify oligozoospermic individuals at risk. in medicine, fish can be used to form a diagnosis, to evaluate prognosis, or to evaluate remission of a disease, such as cancer. treatment can then be specifically tailored. a traditional exam involving metaphase chromosome analysis is often unable to identify features that distinguish one disease from another, due to subtle chromosomal features; fish can elucidate these differences. fish can also be used to detect diseased cells more easily than standard cytogenetic methods, which require dividing cells and requires labor and time-intensive manual preparation and analysis of the slides by a technologist. fish, on the other hand, does not require living cells and can be quantified automatically, a computer counts the fluorescent dots present. however, a trained technologist is required to distinguish subtle differences in banding patterns on bent and twisted metaphase chromosomes. fish can be incorporated into lab-on-a-chip microfluidic device. this technology is still in a developmental stage but, like other lab on a chip methods, it may lead to more portable diagnostic techniques. general process of fluorescent in situ hybridization (fish) used for bacterial pathogen identification. first, an infected tissue sample is taken from the patient. then an oligonucleotide complementary to the suspected pathogen's genetic code is chemically tagged with a fluorescent probe. the tissue sample is chemically treated in order to make the cell membranes permeable to the fluorescently tagged oligonucleotide. the fluorescent tag is then added and only binds to the complementary dna of the suspected pathogen. if the pathogen is present in the tissue sample, then the pathogen's cells will fluoresce after treatment with the tagged oligonucleotide. no other cells will glow. species identification fish has been extensively studied as a diagnostic technique for the identification of pathogens in the field of medical microbiology. although it has been proven to be a useful and applicable technique, it is still not widely applied in diagnostic laboratories. the short time to diagnosis (less than 2 hours) has been a major advantage compared with biochemical differentiation, but this advantage is challenged by maldi-tof-ms which allows the identification of a wider range of pathogens compared with biochemical differentiation techniques. using fish for diagnostic purposes has found its purpose when immediate species identification is needed, specifically for the investigation of blood cultures for which fish is a cheap and easy technique for preliminary rapid diagnosis. fish can also be used to compare the genomes of two biological species, to deduce evolutionary relationships. a similar hybridization technique is called a zoo blot. bacterial fish probes are often primers for the 16s rrna region. fish is widely used in the field of microbial ecology, to identify microorganisms. biofilms, for example, are composed of complex (often) multi-species bacterial organizations. preparing dna probes for one species and performing fish with this probe allows one to visualize the distribution of this specific species within the biofilm. preparing probes (in two different colors) for two species allows researchers to visualize/study co-localization of these two species in the biofilm and can be useful in determining the fine architecture of the biofilm. comparative genomic hybridization comparative genomic hybridization can be described as a method that uses fish in a parallel manner with the comparison of the hybridization strength to recall any major disruptions in the duplication process of the dna sequences in the genome of the nucleus. virtual karyotype virtual karyotyping is another cost-effective, clinically available alternative to fish panels using thousands to millions of probes on a single array to detect copy number changes, genome-wide, at unprecedented resolution. currently, this type of analysis will only detect gains and losses of chromosomal material and will not detect balanced rearrangements, such as translocations and inversions which are hallmark aberrations seen in many types of leukemia and lymphoma. spectral karyotype spectral karyotyping is an image of colored chromosomes. spectral karyotyping involves fish using multiple forms of many types of probes with the result to see each chromosome labeled through its metaphase stage. this type of karyotyping is used specifically when seeking out chromosome arrangements. chromosome evolution human chromosomes painted with dna from mouse chromosome 11 showing hybridization signals on human chromosomes 17, 5, 2, 7, and 22 and some other chromosomes. that is, an ancestral chromosome broke up into multiple fragments that can still be found in many human chromosomes. fish can be used to study the evolution of chromosomes. species that are related have similar chromosomes. this homology can be detected by gene or genome sequencing but also by fish. for instance, human and chimpanzee chromosomes are very similar and fish can demonstrate that two chimpanzee chromosomes fused to result in one human chromosome. similarly, species that are more distantly related, have similar chromosomes but with increasing distance chromosomes tend to break and fuse and thus result in mosaic chromosomes. this can be impressively demonstrated by fish (see figure).