Roche cobas p 512 User manual

Brand: Roche

Model: cobas p 512

Category: Software manuals

Type: User manual

This manual is also suitable for

cobas p 612

Short Guide

Serum TeachIn

QS I

No. 00000028074

Roche PVT GmbH

Maybachstraße 30

D-71332 Waiblingen

Germany

Phone: +49 (7151) 959 22–0

Fax: +49 (7151) 959 22-10

Email: [email protected]

QS I

Disclaimer

This manual is a product of Roche PVT GmbH.

All rights are reserved. No part of this manual may be reproduced in any form (print, photocopy,

microfilm or another procedure) or processed using electronic systems, copied or distributed without

the written permission of Roche PVT GmbH. Roche PVT GmbH assumes no liability for any errors,

omissions or damages resulting from the use of the information contained in this manual.

Neither Roche PVT GmbH nor its subsidiaries assume any liability to the purchaser of this product or

any third parties for damages, losses, costs or expenses incurred by the purchaser or third parties due

to accident, misuse of the product or unapproved modifications, repairs or improvements to the

instrument.

Roche PVT GmbH assumes no liability for damages or disruptions resulting from the use of options or

accessories that are not original PVT-products or that do not have express approval from Roche PVT

GmbH.

Note: All of the product names contained in this manual are trademarks of the respective companies. If

the trademark symbols © or ® are not included, it can not be assumed that the name is an

unregistered product name.

The content of this manual is subject to change without any communicative obligations

by Roche PVT GmbH.

Serum TeachIn V2.4 – 10/2011 6/24

QS I

Changes

Version Date Writer Chapter Page Changes

1.0 01/2003 may all all 1

issue

1.9 03/2008 may all all extension and update

2.0 09/2009 may all all update of all serum images

2.1 03/2010 foe all all textual revision/ 3-D color space

2.2 04/2010 foe

1.2

1.3

important notes added

textual revision of 'Preparations'

2.2.1 04/2011 foe

may

1.1.1

1.5

Intended Use Statement added

update of network connection to QS I

2.3 05/2011 may 1.2, 1.5 9, 20 update of filename

update of table 3 and table 7

2.4 10/2011 May alle alle Renaming PVT to Roche PVT

Serum TeachIn V2.4 – 10/2011 7/24

QS I

Table of Contents

Serum TeachIn...................................................................................9

1.1. Important notes...........................................................................................9

1.1.1. Intended Use Statement..........................................................................................9

1.2. Introduction ...............................................................................................10

1.2.1. Images for Serum TeachIn....................................................................................11

1.3. Preparations ..............................................................................................12

1.4. TeachIn procedure ....................................................................................12

1.4.1. Creation/ recreation of the serum classifier .......................................................12

1.4.2. QS I - Teach in program ........................................................................................14

1.4.3. Adding images to the classifier ...........................................................................15

1.4.4. Verifying the classifier ..........................................................................................16

1.4.5. Classifying images ................................................................................................17

1.4.6. Position in Color Space ........................................................................................18

1.4.7. Moving to trash......................................................................................................22

1.4.8. Exiting the program...............................................................................................23

1.5. Network connection to the QS I...............................................................23

1.5.1. Establish a FTP Connection.................................................................................23

1.5.2. Image folder ...........................................................................................................23

1.5.3. Deleting image data from the QS I system/ archiving image data ...................24

Serum TeachIn V2.4 – 10/2011 8/24

QS I

1. Serum TeachIn

WARNING

When operating the QS I computer the touchscreen must not be used since the

touchscreen is still active on the side of the QNX computer. Operate the QS I

computer only with the keyboard and the trackball.

NOTICE

The program 'Serum TeachIn' runs on the QS I computer. Use the key combination

2 x [Scroll] or [FN] + 2 x [Scroll], where required, to toggle between the QS I and QNX computer.

1.1. Important notes

CAUTION

QS I system results should not be taken as an exact measurement, but rather

as an approximate assignment.

Additional laboratory analysis is required for precise serum analysis.

NOTICE

The customer has to create and maintain the QS I database.

QS I automatically classifies serum as 'good', 'lightly haemolytic', 'strongly haemolytic', 'lipemic' and

'icteric' solely on the basis of a subjective teach-in procedure carried out beforehand by the user.

The teach-in procedure is based upon image data and not upon analytical results, even if analytical

results are used for 'TeachIn'. This means results provided by QS I are qualitative, not quantitative.

1.1.1. Intended Use Statement

QS I Sample Quality recognition is an automated allocation of serum or plasma sample images into 5

different user-defined quality categories ('good', 'lightly haemolytic', 'haemolytic', 'lipaemic', 'icteric').

These quality categories are defined by the user using own reference samples. During the teach-in

process the images of the reference samples generated by the QS I camera are sorted by drag-and-

drop in the different categories and added to the QS I reference database. If a serum sample is

classified as e.g. haemolytic, then it means that the sample appears to have a haemolytic discoloration.

A relation to a later obtained analyzer result (serum index) cannot be established as these are totally

different physical measurement methods. The definition of the categories as well as the drawing of

conclusions lie in the responsibility of the user.

Serum TeachIn V2.4 – 10/2011 9/24

QS I

1.2. Introduction

So that the QS I system is able to reliably allocate the samples to the individual quality levels during

routine operation, a serum classifier must initially be established on the basis of the sample spectrum

of a laboratory.

The program 'Serum TeachIn' provides the user with support when creating and maintaining the serum

classifier. The serum classifier is the part of the QS I software which is responsible for determining the

quality of the processed samples. Reference images for the individual quality levels (these are referred

to as classes) are assigned to corresponding areas for this. The reference images in their entirety are

referred to as learning samples in specialist terminology.

Serum images used for the learning sample required are created by QS I. At the same time, the

system segments a rectangular serum window from the recorded camera image, which allows the user

to view as large as possible a section of the serum present. The size and quality of this window

depends on several parameters such as the type and manufacturer of the tube, the material properties,

overlap by barcode labels or the amount of serum present.

When later, during routine operation, a serum sample is processed by QS I, its serum window is

ascertained. Afterwards, the QS I software compares the color values of this window with the reference

values, established by 'Serum TeachIn', and determines the quality of the serum on the basis of this

comparison.

The quality is expressed as a class for this. The abbreviation is often cited when referring to these

classes.

Class Abbreviation

good quality G

lightly haemolytic H1

strongly haemolytic H2

icteric I

lipemic L

Table 1

Classes, which are given the attributes lightly or strongly, are referred to as 'subclasses'. Thus, for

example, H1 and H2 are subclasses of the class 'haemolytic'.

Normally, several images of each sample are saved. In addition to the unedited images taken by the

camera of each sample, several other images resulting from image processing are saved.

Up to three subfolders are created for each day:

Folder name Content File format

Original Images showing the entire sample tube JPEG

ROI Images of the serum window found Windows Bitmap

Debug Images taken during the installation phase or for error analysis of

the system are saved in this folder. These images remain

unchanged from how they were recorded by the camera.

JPEG und

proprietary

formats

Table 2

NOTICE

If new sample tubes run through the system, the images are automatically saved to the 'ROI' folder.

Only those the images are to be used for 'TeachIn' which have been newly created during the

preparatory stage.

Serum TeachIn V2.4 – 10/2011 10/24

QS I

For 'Serum TeachIn' the images in the folder 'ROI' are used. The file names of the images are

structured as follows: ser_barcode_quality_level_no.bmp

Example: ser_34125640_q1_g1_01.bmp

All serum images are prefixed with 'ser'. In addition to the barcode, the file name also contains

information on the serum quality found.

Quality Level

q0 good g0

g1 lightly

q1 haemolytic

g2 strongly

q2 lipemic g1

q3 icteric g1

Table 3

Serial numbers (no) are used if there are several images or several samples of the same barcode.

Several images of one sample are saved if, for example, QS I rotates a sample in order to enhance

evaluation because the serum window is very narrow.

1.2.1. Images for Serum TeachIn

If the classifier is to be created or extended with new images, these are copied into a folder provided

for this. All folders required by 'Serum TeachIn' can be accessed via the icons on the desktop and the

start bar.

Icons on the desktop

Figure 1 Figure 2

As an alternative, the folders can be opened by clicking on the Windows [Start] button and then clicking

on the respective link in the menu (

Figure 3).

Image database folder

Windows start bar

Figure 3

Serum TeachIn V2.4 – 10/2011 11/24

QS I

Clicking on the link [Image database] takes you to the folder 'image' which contains all the images

recorded by QS I. A subdirectory is created in this folder for the daily routine. The names of these

subdirectories correspond to the date of the relevant day. The nomenclature enables the images

created to appear in chronological order.

Image database folder

Figure 4

Example: 20090409 = YYYYMMDD = 9

of April 2009

1.3. Preparations

NOTICE

20 – 30 samples per class is recommended for best performance. More samples would expend

unnecessary processing power.

It is recommended to make a 'Fullbackup' (see Service Manual) prior to carrying out

'Serum TeachIn', so that the specific changes to the classifier are still available if the system must

be restored.

Reference sample tubes should be kept in the order of the classes for the purpose of later

comparison between the real sample tubes and their appearance on screen.

Real sample tubes can be identified on the basis of the barcode labels and the corresponding file

name stored in the system.

1. Provide a number of sample tubes for each class you want to teach.

2. Visually evaluate the sample tubes and assign them to the individual classes.

3. On a class by class basis, feed the sample tubes into the system for processing.

1.4. TeachIn procedure

CAUTION

Proper reference image distribution is crucial for correct functioning of the

classifier. 'TeachIn' must only be performed by personnel that have received

specific training for that purpose!

1.4.1. Creation/ recreation of the serum classifier

NOTICE

Only those images are to be used for TeachIn which have been newly created during the

preparatory stage.

1. Click the link [Image database] on the desktop.

2. Select a day with whose pictures 'Serum TeachIn' is to be performed.

Serum TeachIn V2.4 – 10/2011 12/24

QS I

Icon on the desktop Subfolders containing saved images

Figure 5 Figure 6

3. Go to the folder 'ROI' for this day.

4. Highlight the relevant images using standard windows functions.

5. Copy the images highlighted into the clipboard using [Ctrl] + [C].

6. Click on the icon [New TeachIn images] on the desktop.

7. Paste the images with [Ctrl]+[V] from the clipboard into the folder.

Serum TeachIn V2.4 – 10/2011 13/24

QS I

1.4.2. QS I - TeachIn program

• Start the program via the start bar by clicking on 'Serum TeachIn' (Figure 3).

Start screen

Figure 7

QS I – TeachIn menu

Choose Images

The list box 'Choose Images' allows to select and display serum images.

Perform TeachIn

NOTICE

20 – 30 samples per class is recommended for best performance. More samples would expend

unnecessary processing power.

By clicking [Perform TeachIn] the serum classifier is recreated through reading in the color values of all

TeachIn samples of all classes from the corresponding areas. The previous classifier is overwritten for

this!

[ ] enables you to scroll to the first page

If an area contains more than 100 images, viewing is subdivided into pages with 100 images each.

[ ] enables you to scroll to the previous page

[ ] enables you to scroll to the next page

[ ] enables you to scroll to the last page

If an area contains more than 100 images, viewing is subdivided into pages with 100 images each.

Serum TeachIn V2.4 – 10/2011 14/24

QS I

not classified

Under 'not classified' you find the images which have been copied as described in section

1.4.1.

The corresponding file name of the images is shown above. The displayed images can be assigned to

new classes at any time. Therefore, you have to move the cursor over the respective image. The

cursor now becomes a gripping hand. When you press the left trackball button it turns into a drip which

can be dragged onto one of the target classes with the left button kept pressed. Once you let go off the

button above a target class, the image is moved to:

Good Quality

Haemolytic (lightly/ strongly)

Icteric

Lipaemic

1.4.3. Adding images to the classifier

Proceed as follows in order to start the program:

• Click on the [Start] button on the lower left of the taskbar using the left trackball button.

• Start the program by clicking on the program icon 'Serum TeachIn' using the left trackball button.

• Under 'Choose Images' select 'not classified'. This contains all images which have previously been

copied into the folder 'New TeachIn Images.

• Drag suitable images into the relevant classes (

Figure 8).

QS I - Serum TeachIn

Figure 8

• After you have added the serum sections to the relevant classes or subclasses you can check

them by selecting a class under 'Select images' and examining these images for homogeneity, i.e.

all images in this class must show similarity in color.

Serum TeachIn V2.4 – 10/2011 15/24

QS I

Strongly haemolytic

Figure 9

• After new samples have been added to the relevant classes, the classifier must be created.

For this, click the [Perform TeachIn].

1.4.4. Verifying the classifier

After reference images have been assigned to all region, the user can check whether the classifier is

now functioning as required. The functions described in this section visualize several properties of the

classifier. Each class is assigned a characteristic color for this purpose.

Color symbolism of the classes

G H1 H2 I L

Table 4

There are functions which can be performed on an image from any region. If the cursor is located

above a serum image, a context menu for this image can be opened using the right trackball button.

Context menu

Figure 10

Serum TeachIn V2.4 – 10/2011 16/24

QS I

1.4.5. Classifying images

Button [OK] Closes the dialog window.

The serum image is classified pixel by pixel and the result is represented in the specific class colors.

The percentage result of this classification is shown at the right of the window under 'Results'. The

percentage data provide good indication concerning how clear, i.e. how good the classification of the

sample is.

Example of a clear result with good = 85.4 %

Figure 11

An unclear result is shown in the figure below.

Example of a unclear result with good = 55.5% and lipemic = 44.5%

Figure 12

An unclear result can have different reasons:

− A very inhomogeneous image with significant brightness changes from the right to the left can lead

to such a result. This may be caused by improper illumination of the QS I camera system.

− The corresponding serums may have ambiguous physiological characteristics. In such cases we

advise against adding the serum images to the sampling.

− It may also be possible that there are very few serum images or that images have been incorrectly

assigned to the sampling. This can be inspected in 'Position in Color Space' (Chapter

1.4.6).

Serum TeachIn V2.4 – 10/2011 17/24

QS I

1.4.6. Position in Color Space

'Position in Color Space' provides a helpful tool in checking the classifier. Serum samples appear in

colored clouds representing the different classes.

The clouds should have sharp-edged outlines in which the samples are uniformly distributed. Within a

class there should be no large gaps between the serum samples. The better these requirements are

met, the better performance of the serum classifier is.

If the result is not satisfactory, the learning sample should be improved by manual re-allocation of

individual serum samples to other classes or deletion of interfering serum samples.

• If you wish to check the position in the color space, right-click the image and select

'Position in Color Space' in the context menu popping up.

Context menu 'Serum TeachIn'

Figure 13

Display of all classes in the color space

Figure 14

The image which has been selected is highlighted by a black point.

If the image belongs to one of the classes G, H1, H2, I or L, the color of the respective class is

additionally shown in the center of the black point.

Serum TeachIn V2.4 – 10/2011 18/24

QS I

Menu and functions

Check boxes

It is possible to prevent all the classes from being displayed at once. This is helpful if you wish to

examine 2 classes which are very close to each other. Classes which are to be blanked out can be

disabled in the corresponding checkboxes G, H1, H2, I, L on the right-hand side of the screen.

Ticked classes are displayed by clicking the [Show Selection] button.

Buttons

[OK] Closes the dialog window

[Show Selection] Ticked classes are displayed

The function shows the distribution of the learning sample in the CIELab color space. In this color

space, the L-axis denotes the brightness while the a-axis runs from green to red and the b-axis from

blue to yellow. Each point in the graphics corresponds to an image of the learning samples. The color

of the point indicates the class of the relevant sample.

If the menu item 'Position in the Color Space' is called up by clicking on an image (point) a great single

3D space is displayed with the coordinate LAB. The axes span the LAB space.

L 0 = black 100 = pure white

a+ red max. 100

a- green min. -150

b+ yellow max. 150

b- blue min. -100

Table 5

The black point shows the position of the sample which this function was started with. The two graphics

can be used to evaluate whether individual classes overlap. Ideally, the classes form a clearly

differentiable scatter plot. If the user moves the mouse over a point, the file name of the relevant

sample will appear between the two graphics. In this way, problematic or incorrectly assigned images

can be detected in the learning sample.

Serum TeachIn V2.4 – 10/2011 19/24

QS I

The three-dimensional space can be rotated by holding down the right trackball button while using the

trackball.

Display of all classes in the color space; rotated to the left

Figure 15

Key functions

The key 'i' (zoom in) allows to zoom in on the origin of the coordinate system.

The key 'o' (zoom out) allows to zoom out from coordinate system.

Display of all classes in the color space; rotated down

Figure 16

Serum TeachIn V2.4 – 10/2011 20/24

QS I

Left clicking on a point causes the corresponding image name to be displayed at the top left margin.

At the same time the related image is presented, starting from the selected point to the top right of the

screen.

Display of a selected sample in the color space

Figure 17

Display of a selected sample in the color space

Figure 18

Serum TeachIn V2.4 – 10/2011 21/24

QS I

The image can now be dragged with the left trackball button kept pressed to one of the sorting fields of

the individual classes (where the cursor becomes a drop symbol). Once you let go of the left button,

the image will be added to this class and the color of the point will change according to the class the

image has been and will be reassigned to.

Figure 19

1.4.7. Moving to trash

In all class areas it is possible to retransfer images to the area 'not classified'.

If you wish to delete an image, right-click the image and select 'Move to Trash' in the context menu

popping up.

The option 'Delete Image' is also available for images in the recycle bin. Images are irreversibly deleted

from the system if selected.

Serum TeachIn V2.4 – 10/2011 22/24

QS I

1.4.8. Exiting the program

CAUTION

Newly added images are not considered by the program if [Perform TeachIn]

hasn't been clicked after the teach-in procedure.

• Make sure you clicked [Perform TeachIn] after you have made changes to the sorting.

• Close all windows which have been opened during the procedure.

• Change to the QNX computer with [FN] + 2 x [Scroll].

• Restart the system that the classifier changes become effective.

1.5. Network connection to the QS I

1.5.1. Establishing a FTP Connection

Within your FTP client, configure a new profile using these parameters:

• Host Address: <the address looked up as described in chapter Software description>

• Host Type: use <automatic> detection

• Initial Remote Directory: /qs1/Host

• User ID and password conform to the credentials used for accessing the system's control

computer on service level.

CAUTION

Do not move or change any files or even so much as navigate outside the

directory /qs1/Host !

You might inadvertently render the system inoperative.

1.5.2. Image folder

The QS I database can be accessed via a network connection. The images of serum samples are

stored under:

\qs1\Application\images\

A new folder for each day with the date of the day is established. The JPEG-images of sample tubes

are saved to a separate subfolder.

The information for the samples belonging to the images is encoded in the file names. The file names

are formed as follows:

Index_orig_tubetype_barcode_liftingheight_quality_level__no.jpg

Example: 0056_orig_14_34125640_5427_2_1__1.jpg

The index begins with 0 each day. Tube type indicates the unambiguous type of tube within the PVT

tube database.

Serum TeachIn V2.4 – 10/2011 23/24

QS I

The quality and level can be interpreted from Table 6

Quality Level

0 good 0

1 lightly

1 haemolytic

2 strongly

2 lipemic 1

3 icteric 1

Table 6

The numbers (no) are only given if there are several images or several samples with the same

barcode. Several images of a sample are saved, for example, if QS I rotates a sample which only has a

narrow serum window, in order to enhance evaluation.

1.5.3. Deleting image data from the QS I system/ archiving image data

QS I stores the image data of the samples for 9 days (default setting). After this period of time, image

data is automatically deleted.

The memory capacity available is checked during every system start and, if necessary, a warning

message is issued on the user interface. If this message occurs, you have to delete the images from

the image database. Alternatively, you can send the images you intend to archive long-term to another

drive.

Serum TeachIn V2.4 – 10/2011 24/24

Roche cobas p 512 User manual

Brand: Roche

Model: cobas p 512

Category: Software manuals

Type: User manual

This manual is also suitable for

cobas p 612

Download PDF

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Roche cobas p 512 User manual

This manual is also suitable for

Roche cobas p 512 User manual

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