Frequently asked questions
This document answeres some of the most frequently asked questions by customers and users of MetaSystems products. Of course such a listing will never be complete, and it is possible that you have a certain question not being answered here. In this case please feel free to send a mail to webmaster@metasystems.de with the subject 'FAQ'.
General Questions
Q: I already own a certain microscope. Can I use it with MetaSystems products?
A: The interactive systems Ikaros and Isis can principally be adapted to any microscope, that provides a camera adaptor ('C-mount'). Many motorized microscopes are supported by Isis to provide full support of automatic filter changing and focus stack capture. For Metafer scanning systems a motorized Carl Zeiss AxioImager Z1 or M1 microscope is required (alternatively the forerunner model Axioplan 2 Imaging can be used). This microscope provides the speed, quality and performance needed for any of the high speed Metafer applications. Please contact us for further details on recommended microscope configurations.
Q: I am living in a country, that does not appear in your contacts list. How can I get a quotation or a demonstration of a MetaSystems product?
A: Please send a mail to info@metasystems.de or call +49 6205 39610 (Germany). Alternatively you may fill the feedback form. We will be happy to help you.
Q: In our institute we already established a patient database system. Is there a possibility to import and export the data to and from Ikaros and Isis to avoid, that data has to be entered twice?
A: Ikaros and Isis provide an integrated case database, which is very flexible and easy to use. Data exchange is possible via exchange definitions, which can be easily adapted to the needs of any external database. If wanted, automated synchronization with the external patient database can be established (depending on the features of the external database, of course).
Q: Which fluorochrome filters do I need for my application?
A: The fluorescence filters in the microscope are used to select the appropriate signal spectra, that are emitted from your specimen. The specificity of the spectra allows to precisely identify the signals that are labelled with a certain fluorochrome. Therefore it is important to know about the application, the probe kits used for
Questions on the CE Mark for MetaSystems Products
The Q&A from the following section are also available for download (ce-policy.pdf).
Q: Are MetaSystems products CE marked?
A: Yes, all systems manufactured and commercialized by MetaSystems inside the EC are 'CE'-marked according to the EC directive 98/79 on 'in vitro diagnostic medical devices'. It is important to understand that CE conformity is not automatically achieved by assembling systems from components having individual CE marks already! One of the prime requirements of the EC directive is that a complete system has to be subjected to the required test procedures (see below) before it may be CE marked.
Q: What are the consequences for MetaSystems products being 'in
vitro diagnostic
medical devices'?
A: The EC directive 98/79 on 'in vitro diagnostic medical devices' had several consequences for MetaSystems to comply with the regulations:
- MetaSystems GmbH is registered with DIMDI (German Institute of Medical Documentation and Information), the German Competent Authority for 'in vitro diagnostic medical devices'.
- MetaSystems GmbH has implemented a quality management system (QMS) in line with EC, ISO and FDA (Federal Drug Administration U.S.A.) regulations. The QMS includes validation of suppliers, extensive software and hardware tests, risk assessment and effective complaint handling procedures.
- Any new system configuration (PC, camera, framegrabber, mot. microscope stage, stage controller boards, etc.) is subjected to electro-static and electro-magnetic compatibility measurements in a certified laboratory as required for CE conformity.
- None of MetaSystems products are related to the assays listed in Annex 2 of the EC directive 98/79. Therefore, the EC directive allows for a 'self certification'.
- The compliance of MetaSystems GmbH with the rules of the EC directive can be audited at any time by the Competent Authority.
Q: Are customers allowed to assemble systems on their own using
MetaSystems
components?
A: Yes, but such a system cannot be CE marked by law! We can only CE-mark systems manufactured by MetaSystems using approved components. Although MetaSystems can provide 'kits' (for example, comprising camera, framegrabber and software), any system assembled from these kits and a non-approved PC will NOT fulfill conformity rules according to the EC directive 98/79. In this instance, MetaSystems is merely a supplier, but not the system manufacturer.
Under certain circumstances, a CE mark is not required for an 'in vitro diagnostic medical device':
- According to EC directive 98/79, Article 1 (5), health institutions
can disclaim the CE mark, if a device is manufactured and used only
within the same institution and on the premises of the manufacturer or
used on premises in the immediate vicinity without having been
transferred to another legal entity.The EC directive does not affect the
right of a Member State to impose further restrictive measures.
In practice, a CE-mark is not required, if your institution is both manufacturer and user (for example, an IT department can assemble the systems for you, but not an external PC store). - If your institution is not located in the EC, but national laws similar to the EC directive may be applicable.
Another alternative would be to implement CE compliant quality procedures. In this case, your institution has to have a working quality system according to EC directive 98/79. In addition, you must implement an evaluation scheme for the devices and demonstrate compliance to the EC directive 98/79, including risk management and safety requirements for electric equipment. If your device will be used as 'for research use only' (according to the 'IVD Guidance: Research Use Only products' (MEDDEV.2.14/2 rev.1), a more simple CE conformity procedure will apply.
In any way, achieving CE conformity is a labor-intensive and costly process, minimizing any potential cost savings from purchasing components from other sources than MetaSystems.
Q: Will MetaSystems support any system assembled from a 'kit'?
A: If you decide to assemble a system from MetaSystems 'kits' and other components, we can provide technical assistance in setting up the system. For example, you could send a pre-configured PC to MetaSystems for a trial installation. But all cost for a trial installation or on-site support will be charged separately. Providing support does not imply that MetaSystems becomes the manufacturer of the system. The legal responsibility for the system still lies with your institution.
Q: Will MetaSystems' warranty cover also systems including 'kits'?
A: Supporting systems of mixed origin is always difficult. When problems occur, it is often difficult to link an observed failure unambiguously to a certain hardware or software component. It is evident, that we can only take responsibility for systems or components provided by MetaSystems. We will admit any warranty claims for these parts only. Any service for other components must be arranged separately. We strongly recommend to set up a contingency plan covering the following issues:
- Is it possible to send the system to MetaSystems for repair or do you need 'on-site' service (workload, turn around time)?
- Do you need a replacement system while your system is off for repair?
- Is there a complete documentation available for the system (incl.operating systems, service releases and patches, all additional software [drivers ],and license codes)?
- Is there a budget allocated for the repair and any potential additional technical assistance required?
Q: Why Dell computer?
A: MetaSystems started using Dell computers more than 10 years ago, and we have been satisfied with the quality of the products and services ever since. Dell computers are covered by a 3-year world-wide warranty supported by a short response time and a 'repair friendly' system architecture.
Metafer Scanning Applications
Q: Metafer scans up to 8 slides unattended (or up to 80, if the external slide feeder is used). Nevertheless, after the scan the system has to be switched off, so that it is not possible to scan over night or over the weekend.
A: Metafer has the possibility to switch off the computer automatically after the scan. If a master/slave power bar is used, it can even switch off microscope, fluorescence lamp and monitor.
Q: Metafer requires the motorized Zeiss microscope Axioplan 2 Imaging. Since this is a very nice microscope also for manual analysis, I would like to use it without the computer in times, when Metafer is not running. Is this possible?
A: Yes. Since Metafer is taking full advantage of the internal microscope functions for focussing and filter changing, there was no need to apply external motors to the microscope. The only connection between microscope and Metafer is one standard computer cable. Therefore the microscope can be used without any restrictions, even if the computer is not running. The motorized stage can be manually driven with two turning wheels for X- and Y-axis, respectively.
Q: Is there a possibility to adapt a Metafer system to different conditions?
A: Yes. Each Metafer software module (MSearch, MetaCyte, RCDetect and CometScan) has an integrated training feature. It helps you to adapt your system to new scanning conditions, i.e., after introducing a new assay in your lab. The new scanning parameters can be stored as a separate file. You may have as many different parameter sets as you want.
Q: How do I train the system to new scanning conditions?
A: In a first step a new set of parameters has to be created. You can either copy an existing set to modify it or create a completely new, empty one. Use a typical slide made with the new assay to capture some image fields into a so called Training Data set (this step is done automatically by the system). In the integrated training software module you can open this set of Training Data and define positive and negative objects (objects you want to be detected by the system and those you want to be excluded). Using this data, the system can automatically optimize the parameters needed to detect the desired objects.
Q: Do I have to train the system for each slide?
A: No. Once you have created a parameter set for a certain type of slides, you can reuse it for each slide of the same type.
Q: How does Metafer MetaCyte cope with poor slide conditions, i.e. fluorescence background?
A: As a part of the classifier, which can be generated with the help of the integrated training feature (see above), powerful image processing algorithms can be applied. Since the algorithms can be tested during the classifier setup, and since they can be applied individually for each single color channel, it is easily possible to enhance the signals and to lower the background intensity.
Q: I have heard, that Metafer MSearch scans metaphases using the 10x microscope objective. Isn't this too low for precise detection of metaphases, and would there be a possibility to scan for metaphases using a, say, 20x objective.
A: The magnification factor, which is used during for the scanning of slides, is defined in the classifier. Of course you can use any magnification lens you like for your assay; all you have to do is to adapt the classiefieres, or train a new one for the new magnification. Nevertheless, as a rule of thumb one can say: the lower the magnification, the faster the system works. Due to our experience the detection of metaphases can be perfectly done with a 10x objective lens, if the high resolution cameras provided with the Metafer system are used.
Q: Since the scanning should be performed at low microscope magnifications (see above), the gallery images of the detected objects are rather small. Do I have to capture the objects in high magnification manually?
A: No. Optionally, each Metafer module can be extended with AutoCapt, a software which is automatically relocating the detected objects and capturing images at high magnifications (MetaCyte already includes AutoCapt). AutoCapt can for example be used for the automatic documentation of metaphases, but it is also an essential part of the automatic dicentric chromosome analysis software DCScore.
Ikaros
Q: Is it possible to compare the chromosomes of different karyotypes and/or cases on screen?
A: Of course. Ikaros provides a very powerful tool named 'Combined Karyotype'. The user can select up to 6 different cases, which are then directly compared on the screen.
Q: Can I annotate my images?
A: Yes. With the annotation function it is possible to annotate the metaphase and the karyotype. Full access to the fonts and colors of the operating system is provided. The users may generate text templates, which can be placed into the image with just one mouse click.
Q: If I capture a metaphase, it looks very nice on screen. Anyway, if I print it, it looks totally different.
A: Ikaros (and Isis, too) offers the possibility to calibrate the monitor and the printer, so that images look the same on both devices. In the General Settings, file System, you can adjust the grey values for metaphase and karyotype, respectively. Once the images are nice on the monitor, change to the file Printer and calibrate the printer in the same way, so that the prints have the same quality like the monitor image. Please refer to the manual, chapter General Settings, for details.
Q: Can I use other karyotype forms than the default one?
A: Select the menu entry Karyotype - Karyotype in the karyotype window to select other karyotype forms. If you press the key INS you get a list with many other karyotype forms, also for other species than human.
The new Ikaros / Isis version 5.0 even provides a karyotype form editor.
Q: I deleted an object from my metaphase image. Later I realized, that the deleted object was actually a chromosome. Do I have to capture the metaphase again?
A: No, of course not. Due to its unique data handling concept, Ikaros (as well as Isis) saves the original image and all the processing steps you have performed. With this strategy it is possible to get back to the originally captured image at any time. Any processing step can also be undone, without undoing the steps performed afterwards. If you deleted an object, which should not have been deleted, the easiest way to undo this step is: a) go back to the function DELETE again. Any deleted object will appear as black shape in the image, b) Simply click with the middle mouse button onto the object, and it will be restored.
Q: Can I measure the chromosome, p-arm and q-arm lengthes with the software?
A: Yes. Once the position of the centromeres is properly defined (this can also be done automatically by Ikaros), the software is able to generate a list of p- and q-arm lengthes. This is very helpful, if you are working with unknown genomes (i.e., plant or animal chromosomes).
Q: Using the case database, how can I find the cases I am looking for?
A: There are several strategies to find and retrieve data from the integrated case database. The fastest method is the right click into the data field you want to search (this can be any data field available). Just enter the search string into the dialogue box and hit the search button. Ikaros will open the next case matching the search criteria. By selecting the entry 'Search All' instead, you can generate a list of all cases, which fulfil the search requirements. In this way you can easily generate lists of all patients having, say, the same karyotype.
Q: Can I change the datasheet according to my requirements?
A: Yes. Since the case database is very flexible, it is possible to change the datasheet. Datafields, which are not needed, may be switched off, any data field may be re-defined for other purposes, and of course it is also possible to change the captions of the field into other languages.
Q: I am working with chromosomes from a rare species. Can I use Ikaros for karyotyping though?
A: Yes. Ikaros is prepared to handle any species. It comes with an integrated karyotype form editor (from version 5.0), that allows for adapting the software to other kayrotypes. However, many karyotype forms for non-human species are already installed in the system.
The new Ikaros / Isis version 5.0 even provides a karyotype form editor.
Isis
Q: How many color channels can I combine in one image?
A: Isis supports up to 9 color channels per image.
Q: I am using a fluorescence probe with 4 fluorochromes. Once captured, Isis always displays just three signals. Why?
A: In order to reduce the time an image needs to be displayed on the monitor, Isis uses RGB colors in the standard working mode. RGB stands for Red-Green-Blue and describes the way how modern computer monitors define the colors, namely as a combination of those three colors. Therefore Isis organizes the colors in tripletts composed by one red color channel, one green color channel and one blue color channel. Once you define the display color of a fluorochrome in the Fluorochrome Settings you have the choice of a color from one out of four color tripletts. The first column of the color selection table displays the red (R) color, the second one the green (G) color and the last one the blue (B) color. The actual display color is independent from this definition (for example is the red channel in the second triplett displayed in magenta). In the Isis RGB mode, it is only possible to display on complete color triplett. Which "red", "green" or "blue" color is displayed, you can select using the color selector on the upper right of the screen. Note, that only one red, green and blue channel, respectively, can be displayed at the same time.
Q: Then, how can I display more than three color channels on the screen?
A: If you want to generate an image with more than 3 color channels, you have to use the powerful false color tools. Create a false color classification for your fluorochrome channels and apply it to your image using the false color menu (please refer to the manual, chapter False Colors, for details). With the new version 5.0 of Isis, there are even more options to display the image in various color modes. Here you may karyotype the metaphase using the inverted (black-on-white) DAPI image, and then display the colored signals on top of it. Or you do all the work in the fasle color mode.
Q: And how do I print or export such a false color image?
A: Since in older versions the main menu is not accessible in the false color display mode, you have to use the keys to activate printing or exporting. Press 'P' to print the image and 'X' to export it. Version 5.0 and above just prints the image as it is displayed on the screen, when clicking on the print button.
Q: If I chose the automatic integration time setting, can I see the time which was used for the acquisition of an image, once it was captured?
A: Yes. simply click onto the histogram icon. You will get a greyscale histogram for each single (color channel) image and the integration time, which was used to capture the image. This tool can be used to identify the reason for poor image quality: if you do not see any signals in the image, but the integration time is quite high (i.e., 10 seconds), most probably the hybridization was not working well, or the wrong filter was used for capturing this color channel.
Q: It is nice to have automatic integration time adjustment, if one wants to have perfect images. But for a certain study I would like to compare the intensities of my signals between different images. If I use the automatic integration time adjustment, this is not possible. Do I have another option?
A: Isis offers three different ways of adjusting the integration time. The easiest way is of course the automatic integration time measurement, that is therefore set as default. But it is also possible to set a fixed integration time (in seconds) for the whole experiment type. Then all color channels in all images will be captured with this time, which makes the conditions comparable between images. If you would like to have an optimal counterstain image, but to compare the signals only, you have to go for the third option and set individual integration times for the fluorochromes. Then you can acquire the DAPI counterstain signal with automatic integration time and the signal channels with a fixed time. In this way you can also combine transmitted light and fluorescent light images, i.e. to have fluorescent signals on a phase contrast background.
Q: I want to eMail some images to a colleague of mine. Which export file formats do you support?
A: Isis (as well as Ikaros) exports images into TIF (Tagged Image
File Format), JPG (Joint Photographics
Expert Group File Format) and BMP (WindowsTM Bitmap)
format.
TIF is the format of choice for archiving important images, since is the most universal
and most widely supported format across all platforms. TIF-images are very detailed, and
the loss of image data due to the coversion to TIF-images is low, if not zero.
JPG-images can be very small, since they are compressed. They are therefore suitable for
eMail and the internet; most of the images on these pages are JPG-files. Nevertheless, the
compression of JPG-images, though it is very strong, is not lossless, which means, that,
the higher the compression rate is, the more image data can not be recovered. The
compression factor and therefore also the quality of the compressed image can be adjusted:
the higher the compression, the lower is the quality. In Ikaros and Isis,
the image quality can be adjusted in the General Settings on the file card Data Exchange,
by setting the image quality to a value between 0% (lowest quality, highest compression)
and 100% (highest quality, lowest compression).
The BMP-file format is the WindowsTM bitmap format, which provides no internal
compression. Therefore BMP-images are rather large. BMP-images can be imported into most
of the programs running under the WindowsTM operating system.
MetaArchive
Q: What is MetaArchive for?
MetaArchive is an automatic backup software, that is delivered with any Ikaros or Isis system. MetaArchive detects, which cases or images were created or modified since the last backup, and copies these cases and images to the archiving medium.
Q: What kind of archiving medium is used for MetaArchive?
MetaArchive uses magneto-optical (MO) disks for the storage of archived data. Therefore each Ikaros or Isis system, that acts as data server, is equipped with a MO disk drive. MO disks are known to be the most secure data storage medium available. They provide full read and write access and are therefore easy to handle. Today a MO disk has a capacity of up to 2.3 GB.
Q: When I add a new preformatted magneto-optical disk to my archive, MetaArchive displays an error message.
MetaArchive uses the internal serial number of the disk for its identification. This serial number is given to the disk by the operating system while formatting. Preformatted disks sometimes do have the same serial number, since they have been copied 1 : 1. Since MetaArchive does not allow two disks with the same serial number, it is necessary to re-format the disks to assign a new serial number to it.
To be continued...
