Frequently Asked Questions - TissueQuest

Is TissueQuest an expert developers software?

  • No, with TissueQuest you can start after a short introduction to run your very own analysis.

What are the minimum system requirements to run TissueQuest on my PC?

  • Operating system Win XP SP2.
  • Intel Pentium 4 processor, 2 GB RAM, 1 TB (1000GB) HD, 2 TFT 19” Screens, DVD multiformat dual layer reader/ writer

What are the antibodies I may/ have to use?

  • All antibodies available on the market are suitable as long as you can get them going

What types of slides can be analysed with TissueQuest?

  • TissueQuest is suitable for all staining types as long as the images can be acquired using a monochrom camera. The number of antibodies or channels you might use is unlimited. You can analyse also cells in culture as well.

What is the recommended thickness of the tissue?

  • The thickness of your specimen ideally lays between 4 to 6 µm. However we have analysed various tissues and cultures with more than 100µm of thickness but please be aware that in such cases you will see cells laying over each other. In some cases the overlaying cells might interfere with your result

Parrafine sections, are they suitable for TissueQuest?

  • • Yes, for sure they are fantastic as long as you can get the antibodies going. You may use TissueQuest also for frozen sections.

Peroxidase stainings, they are fine for TissueQuest?

  • No, TissueQuest is definitively adopted for fluorescence antibodies stained tissues. In some cases you might be able to analyse peroxidase stainins when the images are acquired with a monochrom camera. The best is to use the HistoQuest software suite for IHC stained sections.

Nuclear staining, is this necessary?

  • It’s a nice thing to have and many protocols use DAPI as master channel. However, there are also many situations in which it is better to use the antibody as master channel especially when the stained cells are elongated or of irregular shape. TQ4.0 also offers the opportunity to use total are measurement which is very different from the nucleus based analysis.

Cells without staining, does TissueQuest recognize them?

  • No. A staining of the relevant cellular target structures is a condition sine qua non.

The different colours in the binary measuring masks overlay, what is their meaning?

  • The colorisation of identified cells is randomly done by the analysis software as an aid for detection, the colors have no further meaning for the users.

The scattergrams and their results, may I use them for further analysis as in flow cytometry?

  • Yes, for sure! Users may set cut offs and gates, they can be changed in every respect any time. All relevant changes are displayed just in time for all analysis windows. You might also export your data to excel for preparing some bar charts.

What is the percentage of definitive single cell recognition?

  • In a solid tissue in the moment the discovery rate is more than 93%.

Nuclei with exceptional shapes, elongated or ringshaped, does TissueQuest recognize them?

  • Yes, for sure. The constantly in the background operating dynamical algorithms always are adopting to the staining situation of different cells and structures. However it is fair to say that especially elongated nuclei are often broken into two. Also special low intensity ring structures as nucleus stain are also sometimes broken into pices and might be merged using the merging algorithm in TissueQuest.

The generated results I can be stored?

  • Yes. You also may export your results into different dataformats like Word or Excel.

How about Apple – Macintosh?

  • Sorry, this is not handled in the moment.

Frequently Asked Questions - HistoQuest

Why can no project be created in HistoQuest from the "import folder"?

  • Because the images are not 24-bit
  • Because the images are larger than 3200 x 2400
  • Because the images in a folder are not of the same size

How do I add multiple image folders at once into a HistoQuest project?

  • Use the "Add Subfolder Images" option on the "Import Folder Wizard"

How do I rename a marker in HistoQuest?

  • Tools -> Options -> System Data -> Markers: Rename (for the generic marker names)
  • "Markers" menu on the region detail window for the markers in a project

How do I change the color and the thickness of the backward gated events in HistoQuest?

  • Tools -> Options -> General -> Image Viewer: Overlay

How do I open the "Raw Data" window for backward gated events in HistoQuest?

  • Perform the backward connection and press the “View Raw Data” button on the corresponding region's detail window on the “Results” tab

Why are the overlay images obtained in HistoQuest not shown on a print preview / PDF document?

  • Because there is no cache of the sample

Frequently Asked Questions - TissueFAXS

Why are some TMA spots not acquired in TissueFAXS?

  • Some of them might be placeholders. Set them on NO after the Tissue-autodetect or acquisition and reacquire only these spots

How do I change the maximum "Exposure Time" for the PCO in TissueFAXS?

  • Right mouse click on it and set max value.

Can I change the camera setting for a reacquisition flag in TissueFAXS?

  • No. In order to change the camera settings, the entire region should be reacquired.

Is it possible to "lock" the changes made in Tools -> Options in TissueFAXS?

  • Some of the options already have recommended values. In current versions, users can be created with restricted right (click on “Add User” and set the “Role” of the user). The restricted users won't be able to change sensitive settings.