Image Studio Lite: Tutorial Guide
Image Studio Lite: Tutorial Guide
Image Studio Lite: Tutorial Guide
Tutorial Guide
Image Studio
Analysis Software
Version 4.0
Notice
The information contained in this document is subject to change without notice.
LI-COR MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS
MATERIAL, INCLUDING, BUT NOT LIMITED TO THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. LI-
COR shall not be liable for errors contained herein or for incidental or con-
sequential damages in connection with the furnishing, performance, or use of this
material. This document contains proprietary information that is protected by copy-
right. All rights are reserved. No part of this document may be photocopied, repro-
duced, or translated to another language without prior written consent of LI-COR,
Inc.
Printing History
Publication Number 977-14412
March 2014
4647 Superior Street • P.O. Box 4000 • Lincoln, Nebraska 68504 USA
Technical Support: 800-645-4260 • North America: 800-645-4267
International: 402-467-0700 • 402-467-0819
LI-COR GmbH, Germany (Serving Europe, Africa, and the Middle East): +49 (0) 6172 17 17 771
LI-COR UK Ltd., UK (Serving UK, Ireland, and Scandinavia): +44 (0) 1223 422104
For other countries, contact LI-COR Biosciences or a local distributor.
www.licor.com
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Table of Contents
Getting Started 7
Install the Software 7
Windows® 7, 8, or 8.1 Operating Systems 7
Installing via download: 7
Macintosh® Computers 7
Installing via download: 7
Set up a Work Area 8
Optional Key Tips 8
Image Files 11
Import an Image 11
Export Acquisition Data and Images 12
Image Display 15
View the Image 15
Display 15
Adjust the Image Appearance 17
Features 18
View Mode 18
Slide Show 18
Create 19
Crop the Image 21
Print/Export Area 22
Data Analysis 23
Add and Manipulate Shapes Manually 23
Profiles Tab 25
Auto Adjust 26
Subtract the Background 27
Subtract a User-Defined Background 27
Show 28
Concentration 28
Annotate the Image 29
Tables 31
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Images Table 31
Add or Remove a Column 32
Add Custom Columns 33
Paste Data in a Column 33
Paste Data from a Spreadsheet to a Column 33
Copy Data to a Spreadsheet 34
Sort by Column 34
Filter the Table Manually 34
Filter by Column 35
For more Filter Options… 35
View the Shapes Table 35
Exporting Data 36
Save File 36
Launch Spreadsheet 36
Print 36
Options 37
Reporting 39
Print an Image 39
Create a Lab Book PDF 39
Print a Lab Book 41
Create a Chart 41
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Getting Started
Install the Software
IMPORTANT: You must be logged in using an administrator account. If neces-
sary, log out and log back in using an Administrator account.
Note: Go to www.licor.com/islite and click the Support Materials tab to find the
free software.
Macintosh® Computers
Installing via download:
1. Go to your Mac® System Preferences and click Security & Privacy to open
the Security & Privacy window.
2. Click the lock in the bottom left corner of the window to allow editing, if
necessary.
3. Under the General Tab, click Mac App Store and identified developers
under the Allow applications downloaded from option.
4. Download, and double-click the MacImageStudioLite_4.x.dmg file on your
computer.
5. Click Agree to accept the license agreement.
6. To install, drag the Image Studio icon into the Applications folder
7. Open the Image Studio Application by double-clicking the Image Studio
icon.
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Getting Started
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Getting Started
Press the letter key next to the ribbon tabs to view the ribbon for the selected tab
and the key tips for the commands on that ribbon. Press the letter key next to the
commands to activate the commands or open another menu. For Key Tips with
two letters, press the keys sequentially on the keyboard.
In this manual, instructions refer to selecting tabs and commands with the mouse.
Press Alt at any time to use the Key Tips to select the tabs and commands with
the keyboard.
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Image Files
Import an Image
Tutorial images are provided at www.licor.com/islite in the Support Materials tab.
The folder name for the Western Image is ‘9999999_01’. Follow these instruc-
tions to open the image.
1. Download the image to your computer.
2. Click the Application Menu Button and hover over Import. Hover over
Image Studio and click Zip File.
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Image Files
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Image Files
1. To save the image acquisition, click Image Studio and choose Folder or
Zip File. Click Zip File to save the image acquisition(s) as a compressed
(zip) file. Either choice opens a window where you can select the folder to
which to save the image acquisition.
Note: You can save image acquisitions to another Work Area or create a zip file
to share with another Image Studio user.
2. To save the image to a graphics file, click Single Image View to view a
choice of Current Image, Selected Images in Images Table, or Color Bar
Only. Each choice opens a window where you can select the folder, the file
type (TIFF, PNG, or High Quality JPEG), and resolution.
Note: Images saved as these file types (TIFF, PNG, or High Quality JPEG) are for
presentation purposes and should not be used for further analysis.
3. To save a tiled image file from images in the Table, click Multiple Image
View to open a browse window where you can select the folder, the file type
(TIFF, PNG, or High Quality JPEG) and resolution.
Note: You can quickly and easily save the data in the Tables to a spreadsheet.
Refer to Exporting Data in the Tables chapter.
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Image Display
View the Image
Click the Image ribbon tab to display the Image ribbon.
In the Zoom group click the magnifier icons to enlarge or reduce the displayed
image. You can also scroll the mouse wheel or use the scroll function of a keypad
to zoom in or out.
Display
The Choose Display and Adjust Display Assistants are alternate ways to adjust
the image display.
Click Choose in the Display group and select the 800 channel to open the
Choose Display Assistant.
Click the view with the best display. The Adjust Display dialog will open for fur-
ther adjustment.
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Image Display
Click Adjust in the Display group and select the 800 channel to open the Adjust
Display Assistant.
Select Signal at the bottom left to adjust the maximum point on the curve, Back-
ground to adjust the minimum point, or Midtones to adjust the K value. Click Dim-
mer or Brighter to change the visual appearance of the image. When finished,
click Done.
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Image Display
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Image Display
a. Drag the left (min) dot on each graph to adjust the lower
threshold of pixel values that will shade to the same color on the
viewed image. Shading the lower intensity pixels to the same
color will create a visually cleaner background on the image.
b. The rightmost (max) dot on each graph adjusts the upper
threshold of pixel values that will shade to the same color on the
viewed image.
c. Click and drag the middle dot on each graph vertically to change
the K value.
Note: Changing the visual image will not change the data collected for that image
or the quantification of that data. It only changes the mapping of raw image pixels
to display pixels.
6. Further explanation can be found in the online Help system by clicking the
question mark next to the Curves button.
Features
Click Features at the top right to toggle between showing and hiding features on
the image. Features include text, arrows, lane markers, shapes, and other items.
When Features is highlighted, these objects appear on the image and in all
exports of the image. Click Features to hide these objects from the image and all
exports of the image. To hide these items individually, open the Analysis ribbon
and disable the check box next to the item(s) in the Show group.
View Mode
Select Single in the View Mode group to view and analyze a single image. Click
the Show Multiple Images button and select the number of images to view from
the drop-down menu.
Note: You can not analyze an image in Multiple Image View.
Slide Show
Click Start and the images in the Table will appear in the window sequentially.
Click Stop to return to normal viewing. Click the arrow (>) on the Slide Show
group to open the Slide Show Parameters menu. Choose to display the images in
the Table and stop at the end, or return to the beginning of the table and continue
displaying the images (Loop continuously). Adjust the slider to modify the
amount of time each image is displayed.
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Image Display
Create
Click a button in the Create group to create a new image acquisition file with the
designated action applied. The original image acquisition remains unchanged.
Click Duplicate to create a copy of the image. Click Rotate or Flip to open the
Rotate or Flip Options menu and select an orientation.
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Image Display
Click Free Rotate to open the Free Rotate Options dialog box and click the arrow
buttons to rotate the image clockwise or counterclockwise. Warning: Free rota-
tions change the image data for the new image and may affect quantification res-
ults.
Click Reduce Noise to open the Reduce Noise Options dialog box and select an
option. Hover over each option to open a tooltip explaining the method. Click OK.
Warning: Reducing noise changes the image data for the new image and may
affect quantification results.
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Image Display
Click Align Channels to open the Align Channels menu. Select one channel as
the static reference and adjust the other channel using the arrow buttons. Click
OK.
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Image Display
Print/Export Area
Place crop marks on the image to indicate the area of the image to print or export.
These crop marks can apply to the selected image, or all images in the Images
table.
1. Click Apply and marks indicating the corners of the cropped area appear on
the image.
2. Click Modify to open the Modify Image Print/Export Area dialog. Two boxes
appear as dotted lines on the image.
3. Drag the small box in the middle of the image to center the crop marks. Drag
the corners of the large box to surround the area of the image to print or
export.
4. Click Current Image to mark this image with these crop marks and click
OK. Small crop marks indicating the corners of the cropped area appear on
the image at the new location.
Note: If Images in images table is selected, this crop definition applies to all
images in the Images Table.
Note:Small crop marks appear on the image as long as Apply is selected. The
crop area will apply to any print or export action. To remove the small crop marks
and print or export the full image, click Apply again to toggle it off. You can
change the color of the crop marks by clicking Edit Color in the Modify Image
Print/Export Area dialog.
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Data Analysis
Add and Manipulate Shapes Manually
1. Click the Analysis tab to open the Analysis ribbon. Set the Analysis Type to
Manual.
2. Click Add Rectangle to add a rectangle to the image or Add Ellipse to add
an ellipse. Click in the center of the an area of fluorescence to place the rect-
angle or ellipse around it. After adding the desired shapes, click Select or
press the Esc key on your keyboard to return the cursor to the selection tool.
Note: Shapes are added to all selected channels. To add shapes to only one
channel, make sure it is the only channel selected in the Display panel on the
right.
3. To move or resize a shape, first select the shape by clicking on it once. Dot-
ted lines indicate the shape is selected.
a. To move the shape, drag the four-pointed cursor within the selec-
tion shape.
b. To resize the shape, hover over any corner or side of the shape.
Drag the double-sided yellow arrow to resize.
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Data Analysis
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Data Analysis
d. You can also rotate shapes by selecting them, pressing the Ctrl key on
the keyboard, and scrolling with the mouse.
Profiles Tab
1. Select ‘Shape 2’ by clicking on the shape with the selection arrow until it
changes to a dashed line.
2. On the right side of the screen, click the Profiles tab to view two graphs of
the pixels within a selected shape. The top graph is a cross section of the
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Data Analysis
pixel intensities from top to bottom. The bottom graph is a cross section of
the pixel intensities from left to right.
3. Adjust the size of ‘Shape 2’ by dragging the arrows on the corners of the
shape. Notice how the graph changes.
Note: The small black marks indicate the boundaries of the shape. Move the
shape around the band so that the small black marks are close to the edges of the
peak to capture the entire signal for that band.
Auto Adjust
The software moves selected shapes to fully enclose areas of fluorescence near
the shapes.
1. Drag a rectangle around the shapes to select them. Dotted lines indicate the
shapes are selected.
2. Click Auto Adjust and the shapes will move slightly to better enclose
nearby areas of fluorescence.
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Data Analysis
2. In the pop-up window set the Border Width to 3 and select Right/Left to
select the segments on the left and right sides of the shape for this tutorial.
3. Click Save.
Note: The black line in the Profiles indicates the background that will be sub-
tracted.
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Data Analysis
2. Using what you’ve learned from Add and Manipulate Shapes Manually in
this chapter, place a shape on the image in the region that you have chosen
as the background.
3. Select the shape by clicking on it with the selection arrow so the shape out-
line becomes a dashed line.
4. Click Assign Shape in the Background group.
Show
In the Show group, enable all check boxes, indicating all items will appear on the
image. To specify the location of the labels, click on the arrow at bottom right to
open the Image View Labels menu.
Concentration
You can assign concentration values to two or more shapes or Bands and the
Image Studio software will assign a value to the other shapes or Bands based on
their relative Signal.
1. Click the Shapes tab at the bottom of the table to open the Shapes Table, if
necessary. Add Conc. Std. and Concentration to the Shapes Table by click-
ing Columns and enabling the check boxes and clicking Save.
2. Double-click the Conc. Std. cell for shape 1 and enter 1.
3. Double-click the Conc. Std. cell for shape 4 and enter 9.
4. Click the Concentration tab on the right side of the screen to view the
assigned concentration standards.
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Data Analysis
5. Click the down arrow under Interpolation Method and click Linear from the
drop-down menu to assign a linear interpolation.
6. You can see the concentration values assigned to Shapes 2 and 3 in the
Concentration column in the Shapes Table.
1. Click Add Text in the Text group and click on the image. Type the desired
text in the Text: box. Click OK to add the text to the image.
2. Click Add Arrow and click on the image to add an arrow to the image. Click
Select or press the Esc key on the keyboard to toggle the cursor back to the
selection tool. Click the text or arrow that was added to the image with the
selection tool. A dashed box appears around the text or arrow. Use the tools
in the Font group to change the appearance of the text or arrow.
3. Click Rotate CW or Rotate CCW in the Text group to rotate the text or
arrow.
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Data Analysis
4. Click Edit Text in the Text group to view the Text Properties menu for the
selected item. Insert different text or add a border to the text with this menu.
If the selected item is an arrow, click and drag the sides of the dashed box to
change the size of the arrow.
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Tables
Image data are stored in the folder selected as the Work Area when Image Studio
is opened. The data are easily accessed in the Tables below the image window.
In the Images Table, each row represents one image. Various fields in that row
contain identifying information about the image. These fields are grouped as
columns that can be moved, added, deleted, sorted, or filtered.
Images Table
1. Click the Images tab at the top left of the Table to show the Images Table.
2. Hover the mouse over any row to display a thumbnail picture of that image.
3. Click any cell to select the entire row and display that image in the window.
4. Click the corner button to select all of the images or press Ctrl+A on the key-
board.
5. Right-click any cell to view a menu with options that include duplicate an
image, delete an image, or view the properties of an image.
6. To move a column, drag the column header to the new location.
The fields in each row contain information about the image and are organized as
columns across all of the images. Some of the columns are properties of the
image and cannot be edited. Examples of these columns include Image ID,
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Tables
Acquire Time, Channels, Resolution, and Instrument Name. Other columns can
be edited with information for that image.
7. To edit a field, double-click on the cell so that a cursor appears. If a cursor
does not appear, that field cannot be edited.
8. Add text where the cursor appears. Press Enter when complete.
Note: To easily find images later, enter identifying information in one or more
fields after acquiring an image.
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Tables
2. To add the Experiment column, click the column description to enable the
check box, indicating that column will appear in the table.
3. To remove the Resolution column, click the column description to disable
the check box and remove that column from the table.
4. Click Save. The table now appears as shown below.
Note: You can also right-click the header of any column and select Insert
Column or Remove Column from the pop-up menu to quickly add or remove a
column.
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Tables
2. In the Table, drag the mouse over the cells in the Comment column (or
press the Ctrl key while clicking each cell once) to select the cells to fill with
the data.
3. Click Paste in the top right of the Table, press Ctrl+V on the keyboard, or
use the right-click menu to paste the data in the selected cells.
Sort by Column
1. To sort by any column, click once on the header. The table will be sorted by
that column. Note: No change will be made if the fields in a column are all
the same.
2. To change the direction of sorting, click the header again. Or, right-click on
the header and select Sort Ascending or Sort Descending.
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Tables
Filter by Column
One or more defined filters can be applied to any column to show only the images
of interest.
1. Click Filter at the top right of the Table.
2. Hover over Column to view the drop-down menu of the current column
headings.
3. Click Analysis to filter using the Analysis column.
Note: Right-click on any column header in the Table to view a drop-down menu
for that column.
4. Deselect ICW and Plate by disabling their respective check boxes.
5. Click OK. Only images without ICWor Plate in the Analysis column will
appear in the Table.
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Tables
Exporting Data
Click Save As or Launch Spreadsheet in the Report drop-down menu to pre-
pare or open an ‘.xls’ file with the selected data. Click Options to select the format
of the file and whether to export selected rows or all rows.
Save File
1. Click Report at the top right of the Table to open the drop-down menu.
Choose the file format (text or xls) and whether to export all rows or selected
rows. Click Save.
2. Click Save As to open the Export menu.
3. Browse to the desired destination folder or create a new one. You can also
edit the name of the file.
4. Click Save.
5. The file will be saved in the selected folder.
Launch Spreadsheet
1. Click Report at the top right of the Table to open the drop-down menu.
2. Click Launch Spreadsheet to open the Launch Spreadsheet menu.
3. Browse to the desired destination folder or create a new one. You can also
edit the name of the file.
4. Click Save.
5. An application that uses these types of files will open with the selected data
and corresponding column headings.
Print
1. Click Report at the top right of the Table to open the drop-down menu.
2. Click Print and the document will be sent to the default printer.
3. Select the default printer by clicking the Image Studio Application button,
hovering over Print, and clicking Select Printer.
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Tables
Options
1. Click Report at the top right of the Table to open the drop-down menu.
2. Click Options to open the Report Options menu.
3. Choose the file format and whether to export all rows in the Table or just
selected rows.
4. Click Save.
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Reporting
Print an Image
1. Click the printer icon in the quick access tool bar, press Ctrl+P on the key-
board, or click the Image Studio Application Button and hover over Print.
2. Click Single Image Per Page to print the currently displayed image.
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Reporting
5. Click Header Options to open the Lab Book Header Options menu. You
can select an image to appear in the header, and up to three lines of inform-
ation.
6. Click Page Setup to select the size of the paper and set the margins. Click
Print Preview to view the current lab book. Click Save to create a PDF of
the lab book.
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Reporting
Create a Chart
1. Click the Chart tab on the right of the application window.
2. Click the button at the top left of the Chart view and choose a template from
the drop-down menu.
Note: When you edit the chart, the button will change to Custom. You can save
the edited chart by clicking Save Current Chart Template.
3. You can edit the chart using the buttons on the top right of the Chart view.
a. Type- Choose Bar Chart or Scatter Plot.
b. Data- Specify the data to use in the chart.
c. Options- Select from several scaling options for the y- and x-axes.
d. Labels- Designate a title for the chart and the y- and x-axes.
e. Color- Choose a color style.
f. Export- Select Save As, Print, or Copy.
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