How to Train Colleagues in the Use of Z32 Amphasys Technology

The most important repeating features for the use of the Ampha Z32 to remember.


Picture of Philipp


Hi, my name is Philipp and, for several years now, I work in the Amphasys support team. I graduated in biology and started working at Amphasys more than 6 years ago, initially in the sales team. This work has taken me all around the globe and I liked it a lot. Today, I am concentrating more on the technical and support side and my job is to help customers whenever they have a problem, or if there is an instrument to be installed, maintained, or if a user training is needed. Some of you, dear readers, I have met in person, but I am aware that in the worldwide activities of Amphasys and our affiliated distributors, I have visited only a fraction of all our customers, most of them in Europe. That’s why I decided to write this blog post to transmit my experience to the whole community.

What this Article is About

Why do I want to reach out to all our Ampha Z32 users? Because over the years, we learned that some issues are recurring, and my teammates and I frequently answer the same questions. I thought it would be a great idea to spread the answers to these questions among all our customers.

Here I want to talk about how to train a new colleague.

Here’s why you should continue reading:
  • Increase your efficiency through reduced time needed for the preparation of training content
  • Reduce down-times of your installed Amphasys equipment due to wrong/ untrained handling
  • Learn, how to train your new colleague much faster

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How to Train New Users

In the Amphasys Support Team we realized that often the training organized internally by users for new users focus just on how to prepare a sample and how to perform a measurement. No doubt, these are important aspects but there is more to it. We understand that often there is not enough time to conceive a training in much detail. That is another important reason why I write it down for you. So let us dive directly into the most important aspects to consider when training a beginner.

Support & Maintenance Overview

Check out our Support & Maintenance options!

Hands-on Experience

Nothing can beat hands-on experience. The only way for your new colleagues to learn how to use the instrument and to perform meaningful measurement is to let your colleagues run samples themselves. It sounds trivial but to give your colleague time to learn to use the technology and show how to do measurements hands-on will result in a higher efficiency and fewer downtimes. In the end you save precious time in doing so. In my humble opinion, this hands-on experience should include:

Sample Preparation

This one is rather easy in terms of planning but needs good training and practice. We recommend that trainees should be shown the effects of choosing different flowers or stamens. Let them practice and experience the effect of different samples on the results of the analysis first hand. Only a few examples for that are:

Choice of flowers/ anthers

A good sample preparation starts with good sampling. Flowers are usually not all in the same stage of development neither are all the anthers of one flower. That needs to be considered because ideally what we want is to compare samples as similar as possible. So, when choosing flowers for sampling of different plants, they all should grow at comparable positions at the plant or at least be at comparable developmental stages. The same applies when choosing anthers of a flower or a spike. The important point here is that you decide how the sampling is done and then always apply the same method in order to avoid measuring secondary effects such as differences in developmental stage and the pollen count.


Some species are known for the distinct effect of the daytime on the result of a pollen measurement. Measurements of corn or lettuce pollen, for example, can have a different outcome if the pollen is sampled in the morning or in the afternoon.

Extracting pollen from the anthers

Some species do not easily release pollen, especially if sampling is done early in the flower development. Crushing the anthers completely using a pestle will release the pollen but also will create a large amount of debris in your sample and even damage the pollen you want to measure. To avoid these issues, use the pestle gently to rub the anthers just a little bit against the wall of the sample tube, then drag the tube on a rack to release the pollen.

Separating Pollen from Stamen with wire rack
Separating Pollen from Stamen with mortel

Separating pollen from stamen with test tube rack

Separating pollen from stamen with pestle in test tube

Equilibrating pollen in buffer

Gating can be turned less uncertain and much easier in any cases, if you put the pollen samples in the measurement buffer and let it stay («equilibrate») there for a few minutes. Test if this is the case for your species of interests by performing a time course experiment.  At first, it may seem that your analysis will require more time, but depending on the species, you can prepare the samples in batches – though be careful in timing the equilibration. Also do not underestimate how much easier it will be to place gates if you will have a clear border between viable and dead populations and will no more need to manually adjust the gating for every measurement. In the figure  below you can see what difference this can make:

a comparison of sample plots with different buffer-times

Comparison between sample plots with no (left) and 10 min (right) equilibration time 

By the way, , we also have a video instruction on sample preparation (and several other topics) available on our website HERE.

Just keep in mind that sample preparation itself is not a trivial aspect of your measurement. Depending on the objective of your experiment, sample preparation may even be different for the same species.

Watch our Sample Preparation Tutorial

Check out the Sample Preparation tutorial!

Performing Measurements

There are two aspects that are worth considering. First, the handling of the instrument itself and second the use of the software. On the instrument side, for example, it is important to know that a sample will travel from the sample aspiration tube, through the chip from left to right before ending in the waste bottle.

Fluidic Path Illustration

Fluidic Path

Understanding the fluidic path helps to recognize chip clogging. Check out our troubleshooting quick guide!

On the software side, it is important to learn which are the available functions and where to find them on the AmphaSoft window. HERE you can find a video where the different options and functions can be found in AmphaSoft. Don’t underestimate this point. 

For example, did you ever think about the fact that a successful data analysis starts with a proper zooming of the plots? For experienced users, this is very basic information, so basic that this is an aspect often not explained during trainings. Just as a short reminder, have a look at these two plots. They are the same except for the zoom level. Looks quite different, doesn’t it?

Data Analysis with Amphasoft

Check out the Data Analysis tutorial!

Amphasys Viability Pollen Sample Plot Small
Amphasys Sample Plot Pollen Viability

Sample Plot

same Sample Plot

Software Structure

The most important aspect here is to get the concept of the navigation bar on the left-hand side of AmphaSoft. It is divided into 3 levels:

  • Instrument Control: gives you access to the basic instrument cleaning options, to the software license and other administrative topics, and to some advanced options mainly used for the instrument maintenance.
AmphaSoft Screenshot of Instrument control

instrument control

  • Measurements: gives you a table with the settings for all measurements in your Workspace. It is also often referred to as the Worklist. 


If you want to change settings for a whole column of the Worklist, you can left-click on the header of each column. This will mark the whole column. Then you can do a right-click anywhere in the column and enter the value of choice. Then confirm with Enter and the value will be changed for the whole column at once.

AmphaSoft Worklist Screenshot

measurement table

  • S_1, S_2, S_3, ect., are single measurements. On the left side options for the respective measurement are given. After the measurement is completed you also see the results of the measurement here.
Screenshot AmphaSoft Measurement

single measurement

Daily maintenance

I am well aware that this is kind of a boring topic for some. But with our instrument it is the same as with everything else: If you clean up after yourself you will have an easier life in the end. Teaching your colleagues the importance of daily maintenance routines is crucial in keeping your instrument functioning and in good shape. So here is what everybody, who is using the Amphasys technology, should know about daily maintenance:


This procedure moves water from the reservoir bottle through all parts of the instrument twice. By design it is required at the start of each measurement day. It is also a good routine to run the rinsing program before longer breaks (e.g. lunch time). The rinsing  has a little brother called Flush. It takes place automatically after each measurement to prevent sample carryover and maintain a minimum level of cleanliness of the fluidic path between measurements.


With the Cleaning program the detergent solution AmphaClean is put through the instrument. The process will take approx. 13 min. This should be done at the end of each measuring day. If there are planned breaks of longer than one hour in between measurement sessions, an additional cleaning makes sense. To adhere to a strict cleaning routine is key in keeping the instrument in good shape.

Emptying the waste bottle

The waste bottle will contain all the remains of the measurement done this day: a mixture of the buffer components, water and biological material from the samples. It is an ideal medium for fungus to grow and should be discarded every day.

Cleaning of the sample tube holder

Just wipe the sample holder with DI water and it will be as easy as on the first day to put the sample tube on it.

Storing the chip

All chips should be removed from the instrument once the measurements and cleaning processes are completed. Longer presence of the chip in its compartment can bend down the contact pins of the instrument. The best place to store a chip is a chip box like this.

Box of measurement chips

Box of measurement chips


The disinfection is an extension of the daily maintenance. It is the same process as the cleaning, just that 70% ethanol is pumped through the instrument instead of AmphaClean. Since the Ethanol would damage a normal measuring chip for this process you will need a blue cleaning chip.

Quick Guides Are Your Best Friend

To conclude this blogpost I would like to bring your attention to something that can help you and your colleagues in case you use our technology just occasionally. After some time away from the instrument it is difficult also for experienced users to remember all important aspects. However, there is help for that in form of the quick guides! Those are point-by-point instructions for almost all aspects of using our technology, from the configuration of a new laptop to the preparation of a sample or the daily maintenance procedures necessary to keep the instrument in good shape. All the information is condensed to very easy-to-understand points and often alongside pictures explaining and underlining the respective topic. We sorted the information by topic, so should there be a question regarding what to do in case of a chip clogging, just have a look at the troubleshooting quick guide. These guides are intended to be printed out once, maybe laminated, and put next to the instrument, so they are available instantly, for each user in case of an open question or a problem. And the best is they are available 24/7. All guides are available in English or Spanish for download on our website.

Amphasys Quick Guides

Check out our quick guides!

I hope that I could give you an overview on which topics to consider for the training of new colleagues. Of course if you have more questions or you want to know something more specific please let us know via My colleagues and I are always happy to help you in pursuing your goals.

Contact us!

For feedback and discussion about the findings, if you wish to receive measurement templates or simply to request additional information.

+41 41 541 91 20

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