Automated IHC/ISH slide staining systems

July 1, 2012

In much the same way that you might read Consumer Reports before purchasing a new automobile or television, I present the following review for your evaluation of automated slide staining systems. This article constitutes a “third installment” in a series of articles for MLO that I have written to provide fellow laboratorians with information that is useful in evaluating such systems for immunohistochemistry (IHC) and in situ hybridization (ISH).1 When the first and second were published, in 20042 and 20083 respectively, there were nearly as many automated IHC/ISH slide-staining systems available as there are today, but many of these instruments lacked capabilities that are now considered commonplace. Although readers might find value simply from scanning the comparative Table 1 to gain a more complete appreciation for features and benefits of these instruments, they may consult the previous installments, which can be found at: and

As most readers would likely agree, the “molecular microscopy” techniques of IHC and ISH staining have become essential to the practice of diagnostic histopathology, and are also in widespread use within research and development facilities. Likewise, the automated systems employed for performing these procedures can be found in nearly every medium to large clinical pathology lab. Unfortunately, the simple fact that these techniques and instruments are in widespread use does not automatically ensure that the staining results produced by these instruments are clinically correct. Automation is undoubtedly helpful in relieving laboratory personnel of repetitive activities and improving the reproducibility of results, but the use of automated slide-staining systems brings with it another set of challenges.

At this point, I should acknowledge two important scientific concepts within this field: that automated IHC/ISH systems are, in the end, just robots that can be programmed to perform procedures that can be (and are still) performed in many labs by hand; and that the quality of the final IHC/ISH staining reaction is less a function of the automated system that may be employed than it is of:

  1. the quality of the specimen material (i.e., initial fixation and processing)


  2. the quality of the reagents (i.e., specificity, sensitivity, and stability)


  3. the adequacy and appropriateness of the procedural validation that should be performed


  4. the conscientiousness of the technicians/technologists who perform these procedures and maintain the automated systems; and


  5. the knowledge and skills of the individuals who interpret the results.


Working in the field of anatomic pathology for more than 25 years, it has been my experience that the use of automated IHC/ISH slide-staining systems has been taken for granted. This is made especially clear when we hear the commonly-expressed sentiment that, as a result of the increasing use of automation, the process of performing IHC/ISH has been “dumbed down.” Considering how important the use of IHC and ISH have become in pathology, the individuals involved in application of these techniques should, in my opinion, strive to “smart it up.” There is no doubt that automation is here to stay, but we cannot overlook the fact that the best possible IHC/ISH results can be achieved through gaining additional education in the underlying science and a greater appreciation for appropriate validation, comprehensive quality control, and proper troubleshooting.

Despite claims made by manufacturers (and some end-users) of automated IHC/ISH instruments, there is no perfect system. They all possess various advantages and disadvantages, and the criteria that are used by stakeholders in the instrument-selection process vary from lab to lab. As I outlined in my earlier articles for MLO, automated IHC/ISH slide-staining systems can be described using expressions such as being “open” or “closed,” or as either providing “online” heat-retrieval or requiring an “offline” method.

Another way of looking at developments in this field is in its similarity to what has taken place in personal computing. There was a time when Windows-based computers dominated the market and, in order to be successful, end-users had to develop some proficiency in adding hardware and software (from a variety of competing vendors); such computers are analogous to “open” IHC/ISH systems. In recent years there has been a significant increase in the use of Mac-based computers (and other “personal” devices), which are very easy to operate and often employ proprietary hardware and software; these computers are analogous to the “closed” IHC/ISH slide stainers.

The field of IHC/ISH slide-staining systems is also analogous to that of personal computing in another way, one that is a function of product loyalty and human nature: many people “draw battle lines.” That is, they feel so strongly about one approach that they are unwilling to consider the alternative. Rather than holding fast to such views, it might be helpful to consider the functional capabilities of the currently available instruments as a spectrum—that is, there are varying degrees of practical and conceptual functionality (Figure 1), and operators of these systems often have to sacrifice one capability in order to obtain another.

Figure 1.

For example, so-called “closed” systems that require nearly exclusive use of the same vendors' reagents—which simplifies that vendor's troubleshooting processes—often restrict the operator's ability to design and/or modify staining protocol “templates.” In contrast, “open” systems often allow a great deal more flexibility in protocol design and implementation. In the final analysis, operators of IHC/ISH slide-staining systems will adapt to each system's capabilities and limitations, and learn how to integrate such instruments into their laboratory's workflow.

Among end-users and manufacturers' representatives, probably the most controversial issue is whether or not a system can heat the slides placed on the platform, a capability that allows for heat-induced epitope retrieval (HIER)2 and the denaturation step required for the identification of DNA targets in ISH procedures. The reason for this controversy stems, in large part, from the idea that systems that permit “on-board” HIER provide greater efficiency. Although the ability of a system to perform HIER eliminates the need for laboratory staff to manually manipulate slides, retrieval solutions, and retrieval devices—which usually requires only five to 10 minutes of hands-on time—the total amount of time that slides are processed on systems that possess retrieval capabilities is much greater.

A better way of looking at this (perceived) efficiency may be to consider total throughput, meaning the quantity of slides that can be processed within a given timeframe. For example, two of the instruments that provide on-board retrieval have a maximum capacity of 30 slides, but, because the heat-retrieval process can consume an hour or more of the total run time, such systems can process only between 60 and 90 slides in an eight-hour period. In contrast, two other systems, with capacities of 48 and 50 slides respectively, but lacking on-board retrieval, can (under ideal conditions) process as many as 150 slides in the same time period. In addition, use of off-line HIER reduces the overall cost of producing stained slides.4

Another related and relatively new feature that differentiates the available systems is accessibility, which refers to the ability to place additional slides on the platform once a staining run has been initiated. Just as clinical chemistry analyzers have, for many years, permitted performance of a variety of test procedures on one sample simultaneously, this capability is now available on many IHC/ISH systems, and is referred to as “multi-antigen” or “multiplex” staining.5 There are several approaches to achieving this goal, all of which involve some degree of inefficiency; as a result, this feature may not be as important to end-users as it was intended to be when designed by the manufacturers of these systems.

Finally, there is the issue of whether or not a system's application software includes a specimen/patient identification and tracking function. Although such capabilities may be useful in some cases, most labs that perform IHC/ISH procedures, at least in a clinical/diagnostic setting, already employ a laboratory information system (LIS). Considering that nearly all the available IHC/ISH instruments can be interfaced with the LIS, having this capability included in the IHC/ISH system may not be that important.

A comprehensive comparison of the capabilities provided by the currently available IHC/ISH systems can be found in Table 1. It is my hope that this information will be interpreted as objectively as possible and that the individuals charged with performing an evaluation—which may include members of an organization's Materials Management team—consider more than just the end-users' personal preferences or expectations.


  1. Myers J. Primer for selecting lab equipment. MLO. 2007;39(1):26-27.


  2. Myers J. Automated slide stainers for special stains, immunohistochemistry, and in situ hybridization. MLO. 2004;36 (1);28-30.


  3. Myers J. A review of automated slide stainers for immunohistochemistry and in situ hybridization. MLO. 2008;40(1):41-44.


  4. Myers J. Antigen retrieval: a review of commonly used methods devices. MLO. 2006;38(6):10-15.


  5. Myers J. The technical, clinical, and financial benefits of multi-antigen immuno-staining (MAIS) procedures. HistoLogic. 2006;34(2):25-29.


Joe Myers is a board-certified clinical laboratory scientist and sales professional who currently serves as chair of the IHC Resource Group for the National Society for Histotechnology ( Joe may be contacted at: [email protected].