FujiFilm FLA-7000 User manual

Version 2.0
2006. Mar
Operation Manual

2006. Mar

2006. Mar
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Contents
Contents
Part 1 Preparations Before Use ...................................................................... 1
1. Starting the Image Reader .................................................................................................2
2. About the Main Window .....................................................................................................4
Part 2 Reading Imaging Plates ........................................................................ 5
1. Setting the Reading Conditions..........................................................................................6
2. Setting the IP on the IP Stage ............................................................................................8
3. Setting the IP Stage on the FLA-7000 ...............................................................................8
4. Starting Reading ................................................................................................................9
Part 3 Reading Fluorescent Samples ........................................................... 13
1. Setting the Reading Conditions........................................................................................14
2. Setting a Fluorescent Sample on the FLUOR Stage........................................................17
3. Setting the FLUOR Stage on the FLA-7000 .....................................................................17
4. Starting Reading ..............................................................................................................17
Part 4 Reading Digitized Samples ................................................................ 21
1. Setting the Reading Conditions........................................................................................22
2. Setting a Digitized Sample on the FLUOR Stage.............................................................25
3. Setting the FLUOR Stage on the FLA-7000 .....................................................................25
4. Starting Reading ..............................................................................................................25
Part 5 Lasers and Filters, Other Settings ..................................................... 29
1. Registering Laser and Filter Combinations (Method) .......................................................30
2. Filter Module Settings (Filter Module) ..............................................................................31
2a. Registering Filters in the Image Reader ............................................................................................ 31
2b. Saving the Four Types of Filter Combinations .................................................................................... 34
2c. Recalling Four Types of Filter Combinations ...................................................................................... 35
2d. Registering a New Filter Name .......................................................................................................... 35
3. Other Settings (Preference...) ..........................................................................................36
3a. Settings for Scanning (Scan Settings) ............................................................................................... 36
3b. Selecting the File Format for Saving and the Analyzing Software to Launch (Image File Settings) ... 38
Part 6 Installing and Uninstalling the Software ........................................... 41
1. Installation (For Windows®) ..............................................................................................42
1a. Installation of FUJI USB Control Driver.............................................................................................. 42
1b. Installation of FUJI USB Function Driver............................................................................................ 47
1c. Installation of Image Reader FLA-7000 Software ..............................................................................48
2. Uninstallation (For Windows®) ..........................................................................................49

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2006. Mar
3. Installation (For MacintoshTM) ...........................................................................................50
4. Uninstallation (For MacintoshTM).......................................................................................50
Part 7 Troubleshooting ................................................................................... 51
1. Errors ...............................................................................................................................52
2. Warnings ..........................................................................................................................52

Part
1
Preparations Before Use

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2006. Mar
1. Starting the Image Reader Caution
Please note that the GUI screens may change without notice.
Note1:
The Image Reader FLA-7000 software is available in two types: a
Windows version, and a Macintosh version. Both versions have the
same functions.
This manual uses the screens of the Windows version. If you are
using the Macintosh version, follow the instructions in this manual,
except those of OS-related operations (such as starting and exiting
the software).
Note2:
The following computers are compatible:
OS: Windows XP Professional SP2 or later, Mac OS X 10.3 or later
Memory: 512 MB Interface: USB 2.0
Precautions for Use
Do not connect any USB devices other than the FLA-7000 to the
computer in which the Image Reader is installed. Otherwise, it may
cause malfunction.
During reading, do not use any USB devices other than the FLA-
7000 connected to the computer. If USB devices are used
simultaneously, image data may be lost.
1-1 Turn on the FLA-7000 and peripheral devices.
Caution
If an Imaging Plate is inserted in the FLA-7000 before turning it on,
its scanned data cannot be guaranteed. The sensitivity of the
Imaging Plate may deteriorate, based on the self-diagnosis of the
FLA-7000.
USB
Connection
1-2 Turn on the computer.
1. Starting the Image Reader

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1-3 Make sure that the FLA-7000 has completed the warm-up. (Only
the power lamp on the upper left panel on the front of the FLA-
7000 is lit up when the warm-up is completed.)
Then, perform the procedures below.
For the Windows version:
Start the Image Reader FLA-7000 software from the
Startup menu, or use the shortcut key.
For the Macintosh version:
Double-click the alias or the software to start the
Image Reader FLA-7000 software.
Note:
After starting the Image Reader, its condition is displayed in the
Status area.
• When disconnected:
Cannot recognize FLA-7000. Please check connection and power.
• During warm-up:
FLA-7000 is in self-diagnosis. Please wait.
• When reading is possible:
Ready
1-4 The main window of the Image Reader FLA-7000 software is
displayed.
1. Starting the Image Reader
Software
Shortcut Key
Alias

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2006. Mar 2. About the Main Window
2. About the Main Window
IP Mode
Click when reading
an imaging plate.
Fluorescence Mode
Click when reading
fluorescent samples.
Method
Click this button to
register or erase
combinations of lasers
and filters.
Digitizing Mode
Click when performing
digitizing.
Status
The status of the
FLA-7000 is
displayed.
Ready
The FLA-7000 is
ready for scanning.
Filter Module
Use this button to
change or register the
filter.
Preference...
Use this button to set
the display menu, file
format, or the Log/
Square Root of image
data type.
Filter
The loaded filters
are displayed.
Laser
The conditions of the loaded laser units are
displayed.
In this example, there are four types of laser units
loaded:
LD 670 nm laser,
LD 650 nm laser,
LD 473 nm laser,
LD 635 nm laser.
All the laser units except for the LD 670 nm laser
are ready for operation (OK).
The condition of the LD 670 nm laser shows that it
cannot be used (NG).

Part
2
Reading Imaging Plates

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2006. Mar 1. Setting the Reading Conditions
1. Setting the Reading
Conditions
1-1 Click the button.
The Reader Settings window for the IP mode is displayed.
: Return to the main window from the IP mode.
1-2 Make these settings before reading IPs.
Refer to the following explanations of reading conditions when
making settings.
:
Specify where to save the file after reading.
Click the button.
:
Input the name of a file for saving data of a read image.
You may not start reading unless you input a file name.
:
The comment is saved with the image as a file, and can be viewed
with the analyzing software. Input it if necessary.

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1. Setting the Reading Conditions
Before starting reading, make sure that the LD 650 nm laser is
shown and the IP filter is selected in the Setting field as shown
below.
In IP reading, the LD 650 nm laser and IP filter are selected
automatically.
The laser used for reading is displayed.
The filter used for reading is displayed.
Note:
To use the IP mode, the LD 650nm laser must be loaded, and the IP
filter must be set. If these conditions are not fulfilled, the Reader
Settings window for the IP mode cannot be accessed.
: Click to select from three types of reading sensitivity, as
shown on the left.
: Set the pixel size for reading. Click to select from one of
the 4 types, as shown on the left. A sample with a
smaller pixel size is analyzed more finely.
Short Reading Time Long
Small Image File Size Large
200 100 50 25 µm
: Specify the dynamic range. The dynamic range that can be
detected is bigger with L5 than with L4. If the signals of the
sample are in the L4 range, the density gradation is
represented more finely if L4 is selected.
S10000
Sensitivity: high
Sensitivity: low
S1000

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2006. Mar 2. Setting the IP on the IP Stage/3. Setting the IP Stage on the FLA-7000
Estimated time until reading finishes.
Size of the file.
Drag and select the scanning area on the IP stage.
Note:
Select this to specify the reading area based on the 2.5
cm grid lines on the IP stage.
Select this to specify the reading area arbitrarily.
Select this to specify a reading area of 20 cm x 25 cm.
Select this to specify a reading area of 20 cm x 40 cm.
: Use this button when saving the reading conditions in a file. You
may save reading conditions that are used frequently with this
function and recall them later with .
: Use this button when recalling reading conditions saved with
.
Note:
When starting the Image Reader, the settings information from the
previous session is displayed.
Set the IP on the IP stage.
For instructions on setting the IP, see the Fluorescent Image Analyzing
System FLA-7000 Operation Manual.
Set the IP stage on the FLA-7000.
For instructions on setting the IP stage on the FLA-7000, see the
Fluorescent Image Analyzing System FLA-7000 Operation Manual.
2. Setting the IP on the IP
Stage
3. Setting the IP Stage on the
FLA-7000

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4. Starting Reading
4. Starting Reading 4-1 Click the button to start reading.
The scanned area is displayed in the real-time window, as shown
below.
The stage is read from the left towards the right.
Reading may be finished at any time
before the whole scanning area has
completed reading. Click the
button when you want to
finish reading.
Note1:
If you click Stop during reading, the part that has not been read yet
will be saved as an image with a data value of 0 (light intensity of 0).
Note2:
When you click the button, reading itself is canceled.
You cannot start reading again from the location where reading
stopped.

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2006. Mar 4. Starting Reading
4-2 When you want to change the display parameters of the real-time
window, refer to the explanations below.
: Select the type of tone curve from the pull-
down menu.
Exponential: The exponential tone curve is
used to adjust gradations.
Linear: The linear tone curve is used
to adjust gradations.
Sigmoid: The sigmoid tone curve is
used to adjust gradations.
: Drag the adjuster.
You may adjust the density of the read
image.
Data of a lower light intensity that the line
on the left (Low value) will be displayed as
a completely white image, and data of a
higher light intensity than the line on the
right (High value) will be displayed as a
completely black image.
: If Auto Range Scope is checked, the Image
Reader automatically corrects the optimum
tone.
Note:
The Image Reader converts data read from samples to images that
have an information of 65536 tones, with 0 being the value for white,
and 65535 being the value for black.
The tones are indicated by the horizontal axis of the tone curve
graph.
: You may change the display area by
selecting a magnification ratio from
the pull-down menu. In addition, after
reading, if you click the display area
after clicking the buttons, the
clicked area can be enlarged or
reduced.

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4. Starting Reading
4-3 : Save the data with a different file name.
: Launch the registered analyzing software to
display the image.
4-4 To read a second IP continuously, carry out reading by following
the above procedures.
Click the button to return to the first Reader Settings
window.
Do not open the stage door of the FLA-7000 until the stage has
completely returned. If it is opened, close it immediately. When
scanning finishes, the and buttons
become active, but the button is grayed out until the
stage has completely returned.
4-5 Finish reading.
Before turning off the power of the FLA-7000, shut down the Image
Reader software.

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2006. Mar
Note:
If the photo-multipliers (PMT) are replaced with a multi-alkali PMT,
the IP mode switches from that of the regular IP mode to a PMT
voltage adjustment mode. The PMT voltage adjustment mode differs
from the regular IP mode in that a sensitivity level that matches the
scanned sample can be set independently. Replacement of the
standard PMT with a multi-alkali PMT is done by a serviceman. For
details, contact an authorized dealer.
The Sensitivity settings differ from that of the regular IP mode. The
operation procedures for other settings are the same as those of the
regular IP mode. Follow the operation procedures of the regular IP
mode.
IP mode
PMT voltage adjustment mode
You may set the voltage to be applied to the PMT as an
integral value within the predetermined range. The larger
the value is, the higher the sensitivity, but noise will be
greater.
Small
200V 1000V
Large
Value
Low High
Sensitivity
4. Starting Reading

Part
3
Reading Fluorescent Samples

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2006. Mar 1. Setting the Reading Conditions
1. Setting the Reading
Conditions
1-1 Click the button.
The Reader Settings window for the Fluorescence mode is
displayed.
: Return to the main window from the Fluorescence mode.
1-2 Make these settings before reading fluorescent samples.
Refer to the following explanations of reading conditions when
making settings.
:
Click the button and specify where to save the file after
reading.
Note:
When scanning multiple times, the image data is saved in the folder
with the name specified in File Name, which is automatically created
in the specified location.
:
Input the name of a file for saving data of an image.
You may not start reading unless you input a file name.

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1. Setting the Reading Conditions
Note:
When the number of scans is between 2 and 4, the laser name and
scan number are automatically added to the specified name.
000- 635- 1
File
name Laser
name
Scan
number
Example: If reading is set with the LD 635 nm laser, LD 473 nm
laser, LD 635 nm laser, and LD 635 nm laser, with "test"
as the file name, then the following files are created in the
"test" folder.
test-635-1
test-473
test-635-2
test-635-3
:
The comment is saved with the image as a file, and can be viewed
with the analyzing software. Input it if necessary.
: Scanning can be performed up to 4
times. The following items can be set.
Note:
: From the pull-down menu, select the Method
that corresponds with the sample. The
selected laser and filter combination is
displayed below.
: You may set the voltage to be applied to the
photo-multiplier tube (PMT) as an integral value
within the predetermined range. The larger the
value is, the higher the sensitivity.
Small
200V 1000V
Large
Value
Low High
Sensitivity
: Click the button to increase the number of scans,
and click the button to reduce the number of scans.
Up to 4 scans can be performed.

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2006. Mar 1. Setting the Reading Conditions
: Set the pixel size for reading. Click to select from one of
the 4 types, as shown on the left. A sample with a smaller
pixel size is analyzed more finely.
Short Reading Time Long
Small Image File Size Large
200 100 50 25 µm
: Specify the dynamic range. The dynamic range that can be
detected is bigger with L5 than with L4. If the signals of the
sample are in the L4 range, the density gradation is
represented more finely if L4 is selected.
Estimated time until reading finishes.
Size of the file. Expressed as file size per test x number of scans.
Drag and select the scanning area on the FLUOR stage.
Note:
Select this to specify the reading area based on the 2.
5
cm grid lines on the FLUOR stage.
Select this to specify the reading area arbitrarily.
Select this to specify the entire FLUOR stage as the
reading area.