logos biosystems CELENA S User manual

USER MANUAL
LBSM-MD-ML-CLS-001
VC1712-01
www.logosbio.com

DISCLAIMER
The contents of this document are subject to change without notice.
The CELENA®S Digital Imaging System is an electrical laboratory instrument for scientific research use only.
It is not a medical, therapeutic, or in vitro diagnostics device.
Do not disassemble the device on any occasion as this will invalidate your warranty.
TRADEMARKS
The trademarks used in this document are the property of Logos Biosystems, Inc. unless otherwise specified.
LED Filter Cubes are LTC Licensed Products provided under an intellectual property license from Life Technologies Corporation.
© 2017 Logos Biosystems, Inc. All rights reserved.

2
Table of Contents
Getting Started...................................................................................................................................................................................... 3
Basic Operation .................................................................................................................................................................................... 6
Imaging basics........................................................................................................................................................................................... 6
Iris diaphragm ....................................................................................................................................................................................... 6
Phase annuli .......................................................................................................................................................................................... 6
Imaging control panel......................................................................................................................................................................... 7
Capture images in CAPTURE mode .................................................................................................................................................. 8
Image Editing and Analysis ................................................................................................................................................................. 9
CAPTURE control panel............................................................................................................................................................................. 9
Images panel ........................................................................................................................................................................................ 9
Analysis panel ....................................................................................................................................................................................... 9
Data panel ............................................................................................................................................................................................ 9
Save images........................................................................................................................................................................................ 10
Z-stack Imaging.................................................................................................................................................................................. 11
Z-STACK mode.......................................................................................................................................................................................... 11
Capture images in Z-STACK mode ................................................................................................................................................. 11
View/delete images .......................................................................................................................................................................... 11
Process images ................................................................................................................................................................................... 12
Time Lapse Imaging ........................................................................................................................................................................... 13
TIME LAPSE mode..................................................................................................................................................................................... 13
Capturing time lapse images........................................................................................................................................................... 13
View/save images.............................................................................................................................................................................. 13
Process images ................................................................................................................................................................................... 14
Cell Counting ...................................................................................................................................................................................... 15
AUTOMATED CELL COUNTER.................................................................................................................................................................. 15
Automated cell counter control panel .......................................................................................................................................... 15
Protocol parameters and settings ................................................................................................................................................... 15
Counting cells in automated cell counting mode ....................................................................................................................... 16
View/save results ................................................................................................................................................................................ 16
MANUAL CELL COUNTER ........................................................................................................................................................................ 17
Manual cell counting......................................................................................................................................................................... 17
Saving Images .................................................................................................................................................................................... 17
FILE MANAGER ......................................................................................................................................................................................... 17
Settings ................................................................................................................................................................................................ 18
Settings ...................................................................................................................................................................................................... 18
Maintenance ........................................................................................................................................................................................... 19
Troubleshooting........................................................................................................................................................................................ 20
Safety Information............................................................................................................................................................................... 21
Instrument safety...................................................................................................................................................................................... 21
Personal safety......................................................................................................................................................................................... 22
Instrument symbols .................................................................................................................................................................................. 22
Safety standards ...................................................................................................................................................................................... 22
Product Specifications........................................................................................................................................................................ 23
Ordering Information.......................................................................................................................................................................... 24
Purchaser Notification ........................................................................................................................................................................ 26

3
Getting Started
Product contents
Product contents
Your CELENA®S is shipped with the following components:
Filter cubes (as ordered)
Objectives (as ordered)
Insert plate
Vessel holder frame
Universal Holder
25 mm x 75 mm slide holder, two positions
Power cord with AC adapter
HDMI cable
Wireless mouse
USB drive, 64 GB (includes the user manual and installation guide)
Tool kit
Inspect the product package upon delivery to ensure that all components have been included. If
anything is missing, contact your local sales representative. Damage that may occur during
shipping and handling is not covered by warranty and must be filed with the carrier.
Product description
CELENA®S
Digital Imaging System
The CELENA®S Digital Imaging System is a digital microscope that pairs high-performance optics
and a user-friendly software interface to create a smooth and seamless user experience. Anyone
can obtain sharp and beautifully vivid images in seconds with the CELENA®S.
①Iris diaphragm slider
②Phase annuli slider
③Insert plate
④Vessel holder frame
⑤USB ports (2)
⑥Objective turret wheel
⑦Power button
⑧Focus knobs
⑨Filter cube selection tail
⑩Stage control knobs
4
3
5
6
7
8
9
1
2
8
10

4
Setting up
Unpacking
Lift the CELENA®S out of its box by grasping its base firmly with both hands at diagonally
opposite ends. Place it on a clean, level, and sturdy surface.
Do not hold or lift it by its top cover (where ①and ②are located on the CELENA®S).
Avoid vibrations from other devices.
Leave sufficient space around the instrument for proper ventilation and to prevent
overheating.
Do not expose the instrument to intense ultraviolet light.
Stage assembly
1. Place the insert plate onto the stage with the flat side up and the grooved side down.
2. Move the vessel holder frame arm to the front of the stage using the stage control knobs.
3. Attach the vessel holder frame to the vessel holder frame arm. The frame will snap into
place because of the magnets in the vessel holder frame arm.
4. Move the vessel holder frame to the center of the stage using the stage control knobs.
5. Place the desired vessel holder into the vessel holder frame.
Selection tail guard
The selection tail guard keeps the filter cube selection tail from moving during shipping.
1. Unscrew the screw from the selection tail guard.
2. Pull the selection tail guard away from the instrument. Store in a safe place for future use.

5
Connections
1. Remove the bubble wrap protecting the camera’s USB cable*. Insert into the bottom USB
port at the back of the CELENA®S. Make sure the connection is secure.
2. Plug the wireless mouse dongle into the top USB port at the back of the CELENA®S.
3. Connect an HDMI-compatible monitor to the CELENA®S via the HDMI cable.
4. Insert the connector of the AC adapter into the power inlet of the instrument. Connect the
power cord to the AC adapter. Connect the power cord to an electrical outlet.
Make sure the power cords are appropriate for your region.
Always use power cords and AC adapters provided by Logos Biosystems.
*For the EU version of the CELENA®S, the camera cable is internalized and the inactive D-SUB port has been removed.
Turn ON the CELENA®S
To turn on the instrument, push the power button.
Turn the monitor on.
The initial display will be in CAPTURE mode. The CELENA®S is ready to use.
Shut down the CELENA®S
To shut down the instrument, click the power button located at the top left corner of the screen.
The Z-stage is docked for safety when the CELENA®S shuts down.
In the case of an emergency or system error, push the power button on the front of the
instrument to power off the CELENA®S.
CAMERA
CABLE
Imaging control panel
Date & time
Power button
Settings
Menu-based control panel
Menu bar

6
Basic Operation
Imaging basics
Iris diaphragm
Move the diaphragm slider to adjust the amount of transmitted light to reach the sample.
Opening or closing the iris diaphragm regulates the resolution and contrast of an image.
For transmitted light imaging, slide the diaphragm slider to the left.
This opens the diaphragm to allow in the maximum amount of light and increase resolution.
For optimal fluorescence imaging, slide the diaphragm slider to the right.
This closes the diaphragm to allow in the minimum amount of light and increase contrast.
For automated cell counting, slide the diaphragm slider to the Δ mark (2 cm from the right).
This allows the optimal amount of light for dye exclusion based cell counting.
Phase annuli
The phase annuli slider can be adjusted for brightfield or phase contrast imaging with the three
annuli for transmitted light imaging.
For brightfield imaging, move the phase annuli slider to BF.
For phase contrast imaging at 4X, move the phase annuli slider to Ph1 4x.
For phase contrast imaging at 10X, 20X, or 40X, move the phase annuli slider to Ph2
10x/20x/40x.

7
Imaging control panel
FILTER CUBES panel: The filter cubes panel shows the three
interchangeable filter cubes for fluorescence imaging and one white
filter cube for transmitted light imaging. The selected filter cube is
highlighted in blue. Each filter cube can be renamed and its
pseudocolor selected in the Settings.
To select a filter cube, move the filter cube selection tail in or out.
OBJECTIVES panel: The objectives panel shows the selected objective
and its adjacent objectives. The selected objective is highlighted in
blue. The position, magnification, numerical aperature, manufacturer
and a description of each objective may be modified in the Settings.
To select an objective, turn the objective turret wheel.
Due to the significant differences in objective lengths, take care when
turning the objective turret:
1. Lower the turret by using a preset focus position, the coarse
focus slider, or the coarse focus knob.
Caution! Lower the objective turret sufficiently or the
objectives will hit the insert plate and may be damaged.
2. Turn the turret to the desired objective.
3. Raise the turret using a preset focus position, the coarse focus
slider, or coarse focus knob.
Parfocality correction compensates for deviations along the focal
plane between different objectives. This feature helps maintain focus
when switching to a different objective. The CELENA®S is
precablitrated for the objectives installed at the time of order.
To turn parfocality correction on or off, click Parfocality correction.
Calibrate all objectives when you add or change objectives.
To calibrate:
1. Click LIVE.
2. Turn off Parfocality correction.
3. Place a slide onto the stage.
4. Select an objective.
5. Focus as sharply as possible on the sample and click SET.
6. Repeat with the next objectives.
Important! Parfocality correction can only be used with objectives corrected for the
same vessel bottom thickness (i.e. long working distance objectives cannot be
calibrated with coverslip-corrected objectives).
LIGHT panel: Use the light panel to control the intensity (%), gain (db), and exposure (ms) of the
selected filter cube. The current pixel depth is displayed in the panel and may be changed in the
Settings.
To turn the light source on or off, click the ON/OFF switch.
Light (%) is the intensity of the LED. Gain is the camera’s amplification of the signal. The gain is
analog up to 18 dB, meaning that signal will increase independently of the noise. Values above
18 dB are digital, meaning that both signal and noise will increase. Exposure is the amount of
time that the camera shutter is open to allow light into the sensor.
To adjust values, drag the bars, click the arrowheads, or turn the mouse wheel while hovering
over the sliders.
To colorize images, click Pseudocolor. Pseudocolor can be applied before or after capturing the
image.

8
FOCUS panel:Use the focus panel to focus and to preset focus positions. The preset focusing
speed and distance moved can be adjusted in the Settings.
To focus, manually manipulate the focus knobs or use the sliders in the focus control panel. Drag
the bars, click the arrowheads, or turn the mouse wheel while hovering over the sliders.
Click Fine AF to finely tune focus. The Fine AF Z-scan range can be adjusted in the Settings.
The focus memory feature allows the user to preset focus positions:
1. Move the focal plane to the desired position (move the objective turret) and click the SET
button. The SET button is highlighted in blue when selected.
2. Select the number that you want the position stored on. A keyboard will appear on the
screen. Label the position as desired (e.g. 10X e coli).
Important! Do not touch the focus knobs during the process.
3. Repeat the process for the various positions you want stored. Numbers with stored
positions will be highlighted in blue.
4. Hover over the set numbers to see their labels. Select a number to move the objective to
the preset position.
Preset focus positions may be erased in the Settings.
Capture images in
CAPTURE mode
1. Place the sample into the appropriate vessel holder.
2. Adjust the diaphragm slider as needed.
3. Adjust the phase annuli slider as needed.
4. Select CAPTURE in the menu bar.
5. Select an objective.
6. Select an LED filter cube.
7. Click LIVE.
8. Adjust the light intensity, gain, and exposure as needed.
9. Adjust the focus as needed.
10. Readjust the light intensity, gain, and exposure as needed. Activate the Pseudocolor
function as needed.
11. Capture the image by clicking CAPTURE.
12. Repeat steps 6-10 as needed.

9
Image Editing and Analysis
CAPTURE control panel
Images panel
Use the IMAGES panel to adjust the brightness and
contrast in each channel.
To see the all the channels separately, click Tile. For a
merged image of all the channels, click Overlay. In the
Overlay view, click the thumbnail next to each channel
to hide or show it in the merged image.
Adjust the brightness and contrast of each channel
using the respective sliders or the text boxes.
To undo image adjustments, click Reset.
To delete all captured images, click Clear.
Analysis panel
Use the ANALYSIS panel to add annotations and analyze
captured images using the available tools.
Annotation tools
Select
Angle
Scale bar
Polygon
Text
Ellipse
Line
Segmented line
Rectangle
Freehand
The select tool can be used to select and manipulate
annotations. Right click on an annotation to change properties such as color and size as well as
to copy, paste, and delete the annotation. Double click to deselect the annotation.
The ANALYSIS panel shows the X, Y position of the cursor and the light intensity of that position.
The histogram & line profile is a graphical representation of tonal values. To save individual
histograms and line profiles as a CSV file, click the Export button underneath the graph.
To show or hide all of the annotations made, click the Annotate button.
Data panel
The DATA panel shows you values for measurements
made with the annotation tools in the ANALYSIS panel.
To view all measured values, use the scroll bars.
To clear all measured values, click Clear.
To export measurement data as a CSV file, click Export.