Pyroscience FW4 Microprofiling Software For Microsensor Measurements Instruction Manual

INSTRUCTION MANUAL Profix FW4
MICROPROFILING-SOFTWARE FOR MICROSENSOR
MEASUREMENTS
O2 pH T

FW4 Microprofiling Software For Microsensor Measurements

Profix FW4
MICROPROFILING-SOFTWARE FOR MICROSENSOR MEASUREMENTS
Document Version 1.03
Profix FW4 Tool is released by:
PyroScience GmbH
Kackertstr. 11
52072 Aachen
Germany
Phone +49 (0)241 5183 2210
Fax +49 (0)241 5183 2299
Email [email protected]
Web www.pyroscience.com
Registered: Aachen HRB 17329, Germany

INTRODUCTION

1.1 System Requirements

• PC with Windows 7 / 8 / 10
• Processor with >1.8 GHz
• 700 MB free hard disk space
• USB ports
• Motorized micromanipulator from PyroScience (e. g. Micromanipulator MU1 or MUX2)
• Fiber-Optic sensors for O2, pH, or T in combination with fiber-optic meter with firmware version >= 4.00 from PyroScience (e.g. FireSting®-PRO)

NOTE: Profix FW4 is only compatible with PyroScience devices running with firmware 4.00 or later (sold in 2019 or later). But a legacy version of Profix is still available, which is compatible with older firmware versions.
1.2 General Features of Profix
Profix is a program for automated microsensor measurements. It can read data from two different microsensors. In addition, Profix can control motorized micromanipulators from PyroScience. The central feature of the program is automated microprofile measurements. The user defines the (i) starting-depth, (ii) the end-depth, and (iii) the step size of the desired microprofile. Thereafter the computer will control the complete microprofiling process. The timing-schemes can be adjusted in detail. Automated long-term measurements can easily be set up (e.g. performing a microprofile measurement every hour for several days). If the micromanipulator is additionally equipped with a motorized x-axis (e.g. MUX2), Profix can also perform automated transects measurements. Basic features of the program are:

• Strip chart indicators for display of actual microsensor readings
• Manual motor control
• Manual data acquisition
• Logging at defined time intervals
• Fast microprofiling
• Standard microprofiling
• Automated transects
• Adjustable timing schemes
• Inspection of old data files

SAFETY GUIDELINES

PLEASE READ THESE INSTRUCTIONS CAREFULLY BEFORE STARTING TO WORK WITH THIS PRODUCT

• If there is any reason to assume that the instrument can no longer be operated without a risk, it must be set aside and marked appropriately to prevent any further use.
• The user has to ensure the following laws and guidelines:
  • EEC directives for protective labor legislation
  • National protective labor legislation
  • Safety regulations for accident prevention

THIS DEVICE MAY ONLY BE OPERATED BY QUALIFIED PERSONAL:
This device is only intended for use in the laboratory by qualified personal according to this instruction manual and these safety guidelines!
Keep this product out of the reach of children!
This product is not intended for medical or military purposes!

INSTALLATION

3.1 Software Installation
IMPORTANT: Always perform the installation in the administrator mode!
Download the correct software and Manual in the downloads tab of your purchased device on www.pyroscience.com.
Start the installation program “setup.exe”. Follow the installation guidelines.
The installation adds a new program group “Pyro Profix FW4” to the start-menu, where you can find the program Profix FW4. Additionally, a shortcut is added to the desktop.
3.2 Assembling the Measuring Setup
A standard setup of a microprofiling system consists of (i) a motorized micromanipulator and (e.g. MU1) (ii) a fiber-optic meter (e.g. FireSting-PRO) from PyroScience.
3.2.1 Micromanipulator MU1 and MUX2
IMPORTANT: First install Profix FW4 before connecting the USB cable of the micromanipulator MU1 for the first time to the computer!
Read carefully the instruction manual following with the Micromanipulators MU1 and MUX2. There their assembly, manual operation, and cabling is described in detail. Before connecting the micromanipulator to the power supply, ensure that the manual control knobs on the motor housings are turned into their centre positions (feel the slight detent!). Otherwise the motors would immediately start moving when connecting the power supply! After Profix is started, the manual control knob is by default deactivated, but can be again manually activated within the program.
It is important that you first install Profix FW4 before connecting the USB cable for the first time to the computer. So, if the Profix FW4 installation was successful, just connect the USB cable to the PC which will then automatically install the correct USB-drivers.
3.2.2 FireSting device with firmware 4.00 or later
IMPORTANT: First install Profix FW4 before connecting the USB cable of the FireSting device for the first time to the computer!
FireSting devices are fiber-optic meters for measuring e.g. oxygen, pH or temperature. A broad range of fiber-optic sensor heads are available from PyroScience (e.g. oxygen microsensors). It is recommended to read carefully the user manual of the FireSting device before integrating it into the microprofiling setup.
IMPORTANT: Besides Profix, you also have to install the standard logger software coming with the respective FireSting device (e.g. Pyro Workbench, Pyro Developer Tool), which can be found in the downloads tab of the respective FireSting device on www.pyroscience.com.
This logger software is needed for configuring and for calibration of the fiberoptic sensors before using them within Profix. Please refer to the user manual of the logger software for more information.
NOTE: Profix FW4 is only compatible with PyroScience devices running with firmware 4.00 or later (sold in 2019 or later). But a legacy version of Profix is still available, which is compatible with older firmware versions.

OPERATION INSTRUCTIONS

Remark for the following sections: Words written in bold designate elements within the Profix user interface (e.g. button names).
4.1 Starting of Profix and Settings
After starting Profix the settings in the three tabs (Sensor A, Sensor B, Micromanipulator) of the window Profix Settings have to be adjusted: Profix reads up to two microsensor signals, which are designated within the program as Sensor A and Sensor B. In the tabs Sensor A and Sensor B of the Profix Settings, different fiber-optic meters (e.g. FireSting) can be selected. If only one microsensor will be used, just leave one channel (e.g. Sensor B) as “No Sensor”.
4.1.1 FireSting
If FireSting is selected the following settings window is shown: IMPORTANT: The configuration and the calibration of the sensors connected to the FireSting device must be done in the respective standard logger software coming with this device (e.g. Pyro Workbench or Pyro Developer Tool). The following steps assume that the sensors are already configured and calibrated.
Channel defines the optical channel of the FireSting device to which the microsensor is connected. Analyte indicates for which analyte the respective channel has been configured. If the analyte is oxygen, then the oxygen unit can be selected with the selector Units. The Running Average defines the time interval in seconds over which the sensor signal is averaged.
4.1.2 Micromanipulator
In the tab Micromanipulator of the window Profix Settings, the settings for the motorized micromanipulator can be found.
Select the appropriate Micromanipulator. Angle (deg) is the angle in degrees between the microsensor and the surface normal of the sample under investigation (not available for MUX2). This value is “0” if the microsensor penetrates the surface perpendicular. All depths used by Profix are real depths inside the sample measured perpendicular towards the surface.
The actual distances the motor has to move are calculated by correcting the real depths with the value of Angle. For example if the microsensor penetrates the sample with an angle of 45° and the user wants to move the microsensors 100 µm in depth, the motor actually moves the sensor 141 µm along its longitudinal axis.
For testing and training purposes it is possible to operate Profix without any equipment connected. Just select “No Sensor” under Sensor A and Sensor B, and “No Motor” under Micromanipulator, and check the Simulate Sensor Signal and Simulate Motor boxes. This will simulate oscillating sensor signals, which might be helpful for performing some test runs with Profix.
After pressing OK in the Profix Settings window, a file has to be selected in which the data of the microsensor measurements should be stored. If an existing file is chosen, the user is asked either to append new data to the file or to overwrite it completely. Finally, the main window of Profix is shown.
The settings can be adjusted any time by pressing the Settings button in the main window. When closing Profix, the settings are automatically saved for the next start-up.
4.2 Overview of Profix
The main window of Profix is divided into several areas. The area to the left is always visible and contains the manual control buttons for the micromanipulator (blue buttons), the file handling buttons (grey buttons), and the Settings button (red button). The area to the right can be switched between three tabs. The Monitor tab shows two chart recorders indicating the actual readings of the two channels. The Profile tab is used for manual data acquisition, logging in defined time intervals, fast and standard profiling.
Finally, already acquired data sets can be reviewed in the Inspect tab. The Status Line shows information of the connected motor and the connected microsensors (Sensor A, Sensor B). Here the signal intensity (Signal) of the microsensor readings and the readings from the temperature sensor connected to the FireSting (if used) can be found. Furthermore, the readings of the integrated pressure and humidity sensors are also shown.

4.3 Manual Motor Control

All depth values indicated in the manual motor control box represent the real depth in the sample (see section 4.1.2 under Angle) and are always given in units of micrometers. Actual Depth indicates the current depth position of the microsensor tip. If Goto is pressed, the microsensor will be moved to a new depth chosen in New Depth. If either Up or Down is pressed, the microsensor will be moved one step up or down, respectively. The step size can be set in Step. While the motor is moving, the background of the Actual Depth indicator turns red and a red STOP Motor button appears. The motor can be stopped any time by pressing this button. The velocity of the motor can be set in Velocity (range 1-2000 µm/s for MU1 and MUX2). The maximum speed should only be used for traveling larger distances. For the actual microprofiling measurements speeds around 100-200 µm/s are recommended. A new depth reference point can be chosen by entering a depth value into the control box next to the Set Actual Depth button. After pressing this button, the Actual Depth indicator will be set to the entered value. A convenient way to establish a reference point is to move the microsensor tip to the surface of the sample using the Up and Down buttons with relevant step sizes. When the sensor tip is touching the surface, type “0” next to the Set Actual Depth button and click this button. The Actual Depth indicator will be set to zero.
Assuming also that the correct value for Angle was entered in the settings (see section 4.1.2), all other depth values in the program are now taken as real depths in the sample.
The Manual Control switch allows to enable or disable the manual control knob on the motor housings. These control knobs allow an easy way, for a fast rough positioning of the motors. The maximum speed (control knob fully turned to left or right) is still given by the settings in Velocity. Profix will give an acustical warning (beeps in 1 second intervals), if a motor is operated this way. During a profiling process, the manual control knob is by default deactivated.
REMARK for Micromanipulator MUX2: The program elements described in this section control only the motor of the z-axis (up-down). In order to move the motor of the x-axis (left-right), enable the Manual Control switch and use the manual control knob on the motor housing.
4.4 File Handling
IMPORTANT: Always keep the text file (.txt) and the binary data file (.pro) in the same directory! All data points acquired by Profix are always saved into a text file with the extension “.txt”. This file can be read by common spread sheet programs like ExcelTM. As separator characters tab and return are used. The current file name is indicated in File.
Additionally, Profix generates in the same directory a binary data file with the extension “.pro”. It is important that the text file and the binary data file remain within the same directory; otherwise the file cannot be re-opened in a later Profix-session.
You can choose a new file by pressing on Select File. If an already existing file is selected, a dialog box asks, whether to append or to overwrite the existing data file. The size in kilobytes of the actual file is indicated in Size, while the space left in megabytes on the volume (e.g. hard disk C:) is indicated in Free. Under Comment the user can enter any text during the measurements, which will be saved together with the next data point acquired by Profix.
The data points saved in a file are separated in successive data sets by a header in the beginning of each data set. The header contains channel descriptions, date, time, data set number, and current parameter settings of Profix. The actual data set is indicated in Actual Data Set. A new data set can be generated manually by pressing New Data Set.
The program generates automatically a new data set when a new profile is acquired by the standard profiling process. For a detailed discussion of data points and data sets refer to section 4.6.1.
If a channel is calibrated, the calibrated data are saved in separate columns. These columns are filled with “NaN” (“Not a Number”) as long as the channel is not calibrated.
The uncalibrated data are always saved.
By pressing Check File, a window is opened wherein the current data file is viewed as it would appear in a common spread sheet program. Maximally the last 200 lines of the data file are shown. The content of the window will be updated each time Check File is pressed again.
4.5 The Monitor Tab
The Monitor tab contains two chart recorders for both sensors A and B. The actual reading of each sensor is indicated in the numerical display above the chart recorders.
Depending on the calibration status it is given in not cal. units or in calibrated units.
Each recorder can be switched on and off by pressing the oval ON/OFF button on the left side. The content of the chart recorders can be deleted by pressing the Clear Chart button.  NOTE: The data indicated in the chart recorders are not automatically saved to the hard disk.
There are several possibilities to change the range of the charts. The upper and lower limits of both axes can be changed by clicking with the mouse onto the limit tags, whereupon a new value can be typed in. Additionally, a tool panel is positioned above the chart:
The leftmost buttons X or Y provide auto-scaling for the x- or y-axis, respectively. This feature can also be permanently activated by clicking on the switches leftmost the buttons. The buttons X.XX and Y.YY can be used for changing the format, precision, or the mapping mode (linear, logarithmic).
The upper left button in the right box (“magnifying glass”) offers several zoom options. After clicking the button with the hand, the user has the possibility to click onto the chart and move the whole area while keeping the mouse button pressed. During recording, the chart recorders will automatically adjust the x-range in such a way that the actual reading is visible. It might prevent the user from inspecting older parts of the chart. This problem can be avoided if the chart recorder is momentarily switched off by the oval ON/OFF buttons.
The sensor readings shown in the chart recorders are not automatically saved in the data files. For saving data points periodically, refer to section 4.6.3. However, it is possible to save the actual visible content of each chart recorder by clicking on Save Visible Content. The data are saved in two columns in a text file selected by the user.
The text-file can be read by common spread sheet programs (separators: tab and return). The first column gives the time in seconds, the second column the channel readings.
By clicking with the right mouse button onto the black part of the chart recorder a popup menu appears, offering several functions. Clear Chart removes all old data shown in the chart recorder. Under Update Mode it is possible to select three different modes for the graphics updating, when the visible part of the chart recorder is filled up. In the first mode the visible part is continuously scrolled. The second mode clears the chart recorder and starts again at the beginning, whereas the third mode also starts at the beginning but overwrites the old data. The actual position is indicated by a vertical red line. The items AutoScale X and AutoScale Y function in exactly the same manner as the auto-scaling switches in the tool panel described above.

4.6 The Profile Tab
The Profile tab is used for the actual microprofiling. It contains at the top a small version of the chart recorders already described for the Monitor tab in chapter 4.5. The content of the chart recorders is not saved in the data files. In contrast, the two profile graphs at the bottom show all data points, which are saved, into the data files. To the right of the Profile tab, all control elements are located which are used for manual data acquisition, data logging, fast profiling, standard profiling and automated transects.

4.6.1 About Data Points and the Profile Graphs
Profix provides four different possibilities to acquire data: manual data acquisition, logging at defined time intervals, fast and standard profiling. All four options save the acquired data as “data points” into the data files. Each data point is saved in a separate row of the data file, together with an optional comment written by the user in Comment during the measurement. The data points are grouped into successive “data sets”.
The data points of the last recent 7 data sets are plotted in the profile graphs for sensor A and B, respectively. The y-axis refers to the depth position (µm), where the data points have been acquired. The x-axis refers to the sensor reading. The legend next to the profile graph defines the plot mode of each data set, where the uppermost entry refers to the actual data set. By clicking on an element in the legend, a pop-up menu appears.
The items Common Plots, Color, Line Width, Line Style, Point style, Interpolation can be used to change the appearance of the plotted data points (the items Bar Plot, Fill BaseLine, and Y-Scale are not appropriate to this application). With Clear Oldest Color, the points of the oldest data set can be removed. By repeatedly pressing this button, all data sets except the current one can be removed. This operation does not affect the data file.
The scaling of the profile graph can be modified by the user as described for the chart recorders (see section 4.5). Additionally, a cursor is available inside the profile graph for reading precise values of data points . The actual position of the cursor can be read in the cursor control panel below the profile graph. In order to move the cursor, click onto the cursor button in the tool panel. Now you can click onto the centre of the cursor and drag it to a new position.
By clicking the cursor mode button a popup menu appears. The first three items Cursor style, Point style, and Color can be used to alter the appearance of the cursor. The last two items of the pop-up menu are useful if the cursor is not within the visible part of the profile graph.
If you click Bring to the cursor will be moved to the centre of this window. Choosing Go to cursor will change the ranges of the two axes of the profile graph, so that the cursor appears in the centre.
An additional possibility for moving the cursor is the diamond shaped button .
It allows precise single step movements of the cursor in all four directions.
4.6.2 Manual Data Acquisition
The simplest data acquisition is performed by pressing the button Get Data Point. One data point is read from each sensor.
It is saved directly into the data file and is plotted into the profile graph. A new data set can be created by pressing the button New Data Set (see section 4.4).

4.6.3 Logging at Defined Time Intervals
If the Logger option is checked, data points will be acquired periodically. The period in seconds has to be set in Log every (s). The minimum period is 1 second. Besides the periodical acquisition, the action of the logger is precisely the same as the action of the Get Data Point button (see section 4.6.2).
4.6.4 Fast Profiling
NOTE: Precise measurements of profiles should preferably be performed with the standard profiling function as described in the section 4.6.5.
If both the Logger and the only if moving option are marked, Profix acquires data points (as described in section 4.6.3) only while the motor is moving. This option can be used for acquiring a fast profile. A fast profile is acquired by continuously moving the microsensor tip through the sample while sampling data points in defined time intervals.
It should be emphasized that the acquired data are not precise for two reasons. The position information for each data point is not well defined due to the time delay of the data transmission from the microsensor module. Secondly, the data acquisition takes place while the sensor tip is moving, so it is not really a point measurement. Generally the quality of the fast profiling is increased by lowering the velocity of the motor.
An example for fast profiling is given in the following: A profile between -500 µm and 2000 µm depth in steps of 100 µm should be acquired. First move the microsensor to a depth of –500 µm by using the Goto function of the manual motor control. Adjust the Velocity of the motor to 50 µm/s and set a logging interval of 2 seconds in log every (s).
These values will yield a fast profile with 100 µm steps between the data points. Now check first the only if moving box, followed by checking the Logger box. Use the Goto button again for moving the microsensor to the depth of 2000 µm. The motor will start moving and the fast profile will be acquired. The acquired data points will be directly viewed in the profile graph. If you want the fast profile to be saved as a separate data set, remember to press New Data Set (see section 4.4) before starting the profiling.

4.6.5 Standard Profiling
The lower right area of the Profile tab contains all controls for the standard profiling process, i.e. the motor moves the microsensor stepwise through the sample and acquires at each step one or more data points. All depth units are given in micrometer. The  following parameters have to be defined before starting a profile. Start is the depth where the first data points for the channels A and B are acquired. End is the depth where the profiling process finishes. Step defines the step size of the profile. When a profile is finished, the microsensor tip is moved to the Standby depth.
Because microsensors have a certain response time, the Resting Time after Reaching Depth has to be adjusted. It determines the time in seconds the microsensor tip rests after reaching a new depth, before the next data point is read. If several profiles should be acquired automatically, the appropriate Number of Profiles can be chosen. The microsensor tip is moved to the Standby depth between successive profiles. In Pause Time the resting time (in minutes), before the next profile is performed, can be adjusted.
The profiling is started by pressing Start Profile. The profiling process can be followed by the five indicators with the dark grey background: The indicator to the right of Number of Profiles displays the actual profile number. The other two indicators act as “count-down” indicators, i.e. they show how much time is left of the resting time. The currently active resting time (i.e. either Resting Time after Reaching Depth or Pause Time between Profiles) is indicated by a red background of the respective “count-down” indicator.
A STOP Profile button and a Pause button appear during profiling. The profiling process can be aborted at any time by pressing STOP Profile.
Pressing the Pause button causes the profiling process to halt, but it can be resumed any time by pressing the Resume button.
4.6.6 Automated Transects
If the micromanipulator is equipped with a motorized x-axis (left-right, e.g. MUX2), Profix can acquire also automated transects. A transect consists of a series of microprofiles, where the x-position in between each microprofile is moved by a constant step. The following example explains how to acquire an automated transect across e.g. 10 mm with a step size of 2 mm:

1. Enable the Manual Control switch (see section 4.3) and use the manual control knob on the motor housing for adjusting the starting x-position of the microsensor. The automated transect will start at this x-position, which will be set to 0 mm in the saved data file.
2. Adjust the parameters of the single profiles as described in the previous section.
3. Check Automatic Transect.
4. Adjust Step (mm) to 2 mm.
5. Adjust Number of Profiles to 6 (corresponding to a total x-displacement of 10 mm for a step size of 2 mm)
6. Press Start Profile.

The single microprofiles of the transect are saved in separate data sets (see section 4.4).
The x-position of each microprofile is written in the header of each data set.

4.7 The Inspect Tab
The Inspect tab provides several options for reviewing and analysing acquired data sets.
The data set, which should be plotted in the profile graph, is selected in Sensor A/B and Data Set. The scaling, range, cursor, etc. of the profile graph can be adjusted in the same manner as already described for the profile graphs in the Profile tab (see section 4.6.1).
If older data files should be inspected, the user has to open the respective files by pressing the Select File button and choosing “append data file” (see section 4.4). Pressing the Update button will refresh the graphs after a new file has been selected. The inspect tab provides a simple way for calculating areal fluxes with help of a linear regression. Enter the depths for the Slope Start and the Slope End defining the depth interval of the linear regression. Click the Calculate Flux button and the result of the linear regression is shown in the plot as a thick red line. By adjusting the Porosity and the Diffusivity Do the calculated areal flux will be shown in Areal Flux. Note that these calculations are NOT saved to the data file!
By pressing Create Input File for PROFILE it is possible to generate for the currently shown profile an input file for the profile analysis program “PROFILE” from Peter Berg: Refer to the PROFILE manual for details about adjusting the parameters. Please contact Peter Berg under [email protected] for obtaining a free copy and documentation of his PROFILE-software.

TECHNICAL SPECIFICATIONS

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CONTACT
PyroScience GmbH
Kackertstr. 11
52072 Aachen
Deutschland
Tel.: +49 (0)241 5183 2210
Fax: +49 (0)241 5183 2299
[email protected]
www.pyroscience.com 

References

• Sensor technology - PyroScience GmbH
• Sensor technology - PyroScience GmbH
• Sensor technology - PyroScience GmbH

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