Zeiss LSM-900 confocal Airyscan microscope

Desmarais Building, Room 2234
Advanced Microscope Tier 2 usage price
Instrument awarded to Dr. Jean-Philippe Gratton by the Canadian Foundation for Innovation (CFI # 34992)

in 2015

Applications

Inverted microscope
Airyscan super-resolution with joint deconvolution
Point scanning confocal
- Brightfield
- Phase contrast

Transmitted light

Phase Contrast

- Interference Contrast (DIC)
- Fluorescence

Laser scanning confocal

Airyscan super-resolution

Targeted photo-modulation FRAP
Incubation
Timelapse imaging
Deconvolution
Extended Depth of Focus

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id	Instrument Tabs
title	Zeiss LSM900
direction	horizontal

User Guide

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idtitle	Description	title

id

Description

Light sources

LED lamp for transmitted light
Laser 405nm, 488nm, 561nm, 640nm

Expand

title	Complete specifications

30252545

Emission (nm)	Nominal power Power (mW)	Measured Power (mW)
405	5
488	10
561	10
640	5

X-Cite 120LED mini for visible fluorescence

Expand

title	Complete specifications

Filter (nm)	Emission Peak (nm)	Nominal

power

Power (mW)	Measured Power

at the sample

(mW)
DAPI	365
GFP	470
mPlum	587

Image Added

View file

name	XCite_120LEDmini_Datasheet.pdf
height	250

Objectives

5x/0.15 Ph1 Air
10x/0.25 Ph1 Air
20x/0.80 Air
40x/0.95 Air
40x/1.4 Oil
63x/1.4 Oil

Expand

title	Complete specifications

Position

Name

Brand

Full name

Identifier

Magnification

Numerical aperture

Immersion

Type

Working distance (mm)

Transmittance

(% [nm])

Applications

Coverglass thickness (mm)

1

5x/0.15

Ph1 Air

Air

Zeiss

5x/0.15 Ph1

Air

N-AchroPlan	420931-9911-000	5x	0.15	Air	N-AchroPlan	12.0	Not Available	BF, PhC, Fluo	0.17
2	10x/0.25

Ph1

Air

Zeiss

10x/0.25 Ph1

Air

N-AchroPlan

420941-9911-000

10x

0.25

Air

N-AchroPlan

6.5

Not Available

BF, PhC, Fluo

0.17

3

20x/0.8
Air

Zeiss

20x/0.8

Air

Plan-Apochromat

420650-9901-000

20x

0.8

Air

Plan

-

Apochromat	0.55	>90% [400-800]	BF, DIC, Fluo	0.17
4	40x/0.95 Air	Zeiss	40x/0.95

Air

Plan-Apochromat

420660-9970-000

40x

0.95

Air

Plan

-

Apochromat

0.25

>80%
[410-820]

BF, DIC, Fluo

Variable

	0.13-0.21
5	40x/1.4 Oil	Zeiss	40x/1.4

Huile

Plan-Apochromat

420762-9900-000

40x

1.4

Oil

Plan

-

Apochromat

0.13

>80%
[500-850]

	BF, DIC, Fluo	0.17
6	63x/1.4 Oil	Zeiss	63x/1.4

Huile

Plan-Apochromat

420782-9900-799

63x

1.4

Oil

Plan

-

Apochromat

0.19

>80%
[440-710]

BF, DIC, Fluo

,

Super-Resolution
Strehl ratio >90%

.

0.17

BF: Bright-field
PhC: Phase Contrast
DIC: Differential Interference Contrast

Filter cubes

Filters

GFP
DAPI
mPlum
DIC Analyzer
Empty-
Empty-

Expand

title	Complete specifications

Position	Name	Brand

Identifier

ID	Excitation	Dichroic	Emission	Graph
1	GFP Filter Set 38	Zeiss	000000-1031-346	BP 470/40	FT 495	BP 525/50	Image Modified
2	DAPI Filter Set 49	Zeiss	488049-9901-000	G 365	FT 395	BP 445/50	Image Modified
3	mPlum Filter Set 64 HE	Zeiss	489064-0000-000	BP 587/25 (HE)	FT 605 (HE)	BP 647/70 (HE)	Image Modified
4	DIC Analyzer	Zeiss	424937-9901-000	-	-	-	-
5

Vide

-	-	-	-	-	-	-
6

Vide

-

Detectors

2x Gallium Arsenide Phosphid (GaAsP) Photomultiplier Tube (PMT)
1x transmitted light Electronically Switchable Illumination and Detection module (ESID)
1x Airyscan detector for 63x objective

Tabs Page

Expand

title

User Guide

Complete specifications

Image Added

Tabs Page

title	User Guide

User Guide

UI Expand

title
expanded	true

UI Expand

expanded	true
title	Startup

If not already done, turn on the computer (#1) and

use your

UdeM credentials

to

log in to Windows using your UdeM credentials
Remove the dust cover from the microscope
Turn on the System (#2) and Components (#3) switches in the rack below microscope
Turn on the laser key (#4) in the rack below the microscope
When using the instrument for the first time, it is necessary to import the microscope

-specific parameters BEFORE starting

configuration into the software. See the First Use section below.
Start Zen

Running this procedure will

delete

erase all your experiment protocols and

restore

reset the software to its original settings (ask for support if you are not sure).

If Zen is open, close

Zen

it and wait

for

until it

to close

has completely shut down (this may take up to 30 seconds)
On the Desktop, open the Softwares

folder

folder
Double-click Zen Settings for

LSM900

LSM 900
A script will run and a black window will appear briefly

Click

OK

to close the message

When the message Settings for Zen have been imported successfully

.

appears, click OK to close it
You can

then

now open

Zen

Zen

UI Expand

title	First Use

Please note,

When using the instrument for the first time, it is necessary to import the microscope -specific parameters configuration into the software. This procedure is usually carried out during the training session. However, it is also possible to use it can also be used to reset the software if it is does not displayed display correctly, for example.

Note

UI Expand

title	Loading samples

During this procedure, you will:

Set

This procedure puts

the microscope

in

to a safe configuration

and performs

Perform a calibration
Load your sample
Find and adjust the focus

Once completed, your sample .At the end of this procedure the microscope will be ready for acquisition.

On the microscope touch screen::

If not already done, press Home>Microscope>Control>Objectives>5x to select the 5x objective

In Zen:

Click Calibrate Now

If not already done, select the lowest-magnification objective. On the microscope touch screen Home > Microscope > Control > Objectives > 5x
In Zen, once it has started a calibration dialog should appear. Simply click Calibrate Now.

The microscope will lower the objectives, perform

a

an XY calibration

and then

first, followed by a Z calibration, and then return to its original position.

UI Expand

title	Calibration

This step is required to calibrate the microscope in XY and Z. Doing a calibraiton will save you a lot of time to find your focus or Performing this calibration will significantly reduce the time needed to locate and focus on your sample.

UI Expand

title	Calibration within the Zen Software

note

Tip

Once calibrated, the focus

can be

is typically found at Z = 1.7 mm

)

for a microscope slide.
The Z

value

position can be

found

viewed on the microscope touch screen

Home>Z-Position

UI Expand

title	Calibration with the touch screen

under Home > Z-Position, as well as in Zen within the Focus tab, located on the right side of the screen.

Expand

title	The calibration dialog did not appear...

The system may already be calibrated. This can occur if a previous user calibrated the system and left it on.

On the microscope touch screen:

If not already done, Press Home>Load Position to lower the objectives to the lowest position

UI Expand

title	Verifying if the system is already calibrated

In Zen, within the Focus tab, located on the right side of the screen:

Click Load to lower the objective
The Z position is indicated below Current
If Z position value is less than 100 um the system is calibrated

On the microscope touch screen:

Lower the objective by pressing Home > Load Position

Press Set Work Position to store this position
If necessary,

move

slightly adjust the focus

slightly up

upward to

remove

clear the Lower Z

limit reached

Limit Reached message displayed on the

touchscreen

If not already done, press Home>Microscope>Control>Objectives>5x to select the 5x objective

If asked, tap Done to remove the oil lens cleaning warning

Press Home>Microscope>XYZ>Position>Z-Position>Set zero>Auto to perform focus calibration

Press OK to start the calibration procedure

Wait a few seconds for the calibration to be completed

Press Home>Microscope>XYZ>Position>XY-Position>Set zero>Auto to perform a stage calibration

Press OK to start the calibration procedure

Wait a few seconds for the calibration to be completed

Note
Once calibrated, the focus can be found at Z = 1.7 mm). The Z value can be found on the microscope touch screen Home>Z-Position

UI Expand

title	First focus

touch screen
The Z position value is indicated
If the value is less than 0.1 mm then the system is calibrated

UI Expand

title	Manual calibration with the software

In Zen, within the Stage tab, located on the right side of the screen:

If not already done, check the Show All option
At the bottom of the tab click Calibrate
A warning message will show up click Continue
The microscope will lower the objectives and perform a XY stage calibration and then return to its original position.

In Zen, within the Focus tab, located on the right side of the

Warning

title	Important

Make sure to calibrate the focus before performing the first focus.

On the microscope touch If not done already, press Home>Load Position to lower the objective to the lowest position and press

screen:

If not already done,

press Home>Microscope>Turret>Objectives>5x to select the 5x objective

Info

The 5x objective is the safest because it has the longest working distance (12mm). The sample will appear perfectly sharp long before the lens approaches it. It is recommended to always first focus with the safest lens. The objectives are parafocal, focusing with the safest objective will then allow you to easily find your sample with another objective. The 10x objective is also safe because its working distance is 6.5 mm.

check the Show All option
At the bottom of the tab click Calibrate
A warning message will show up click Continue
The microscope will then perform a Z calibration and then return to its original position

XY and Z calibrations are now complete

UI Expand

title	Manual calibration with the microscope touch screen

On the microscope touch screen:

Navigate to Home > Microscope > XYZ > Position > Z-Position > Set Zero > Auto to perform focus calibration
Press OK to start the calibration procedure
Wait a few seconds for the calibration to complete
Lower the objective by pressing Home > Load Position
Press

Set Work Position to store this position
If necessary,

move

slightly adjust the focus

slightly up

upward to

remove

clear the Lower Z

limit reached

Limit Reached message displayed on the

touchscreen

Place the test slide on the microscope stage with the coverslip toward the objective

Note

title	Important

Always use the test slide to perform the first focus.

If necessary, move the stage so that the sample is centered on the objective

On the computer:

Open Zen

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP, mPlum) to activate the configuration

Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp

Note
Once calibrated, the focus can be found at Z = 1.7 mm). The Z value can be found on the microscope touch screen Home>Z-Position

In the Locate tab, select Off to turn off the illumination

touch screen
Navigate to Home > Microscope > XYZ > Position > XY-Position > Set Zero > Auto to perform a stage calibration
Press OK to start the calibration procedure
Wait a few seconds for the calibration to complete

XY and Z calibrations are now complete

UI Expand

title	Ensuring the calibration dialog is displayed at startup

In Zen:

In the menu bar, navigate to Tools > Options
Select Startup/Shutdown
Under Stage/Focus Calibration, ensure Request Stage/Focus Calibration on Startup is checked
Click OK to close the Options dialog

After performing the first focus, on the microscope touch screen:

Press Home>Microscope>Control>Objectives, press 10x, 20x or 40x to select the desired objective

UI Expand

title	Initial focus

Warning
Ensure that the calibration has been completed beforehand. Calibration will significantly reduce the time required to locate and focus on your sample.

On the microscope touch screen:

If not already done, select the lowest-magnification objective Home > Microscope > Control > Objectives > 5x

Info
The 5× objective is the safest to use due to its long working distance (12 mm). The sample will appear in sharp focus well before the objective approaches it. It is recommended to always focus using the safest objectives first. Since the objectives are parafocal, focusing with the safest objectives will facilitate locating the sample when switching to higher-magnification objectives.

Lower the objective by pressing Home > Load Position
Press Set Work Position to store this position
If necessary, slightly adjust the focus upward to clear the Lower Z Limit Reached message displayed on the touch screen
Place the test slide on the microscope stage with the coverslip facing the objective

Note
Using a test slide will significantly reduce the time required to set up the instrument.

If necessary, adjust the stage to ensure that the sample is centred under the objective

In Zen:

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP or

UI Expand

title	Seconday focus

Warning

title	Important

First focus with the safest objective before selecting another lens and continuing with secondary focus.

UI Expand

title	Focusing with air objectives

Info
The 40x objective is the best Air objective because it has the greatest number of optical corrections (Plan Apochromat) and the largest numerical aperture (0.95) but has a smaller field of view. The 20x/0.8 objective offers the best compromise between Resolution and Field of View

Note
There are two (2) 40x objectives, make sure you select the Air 40x

In Zen :

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP,

mPlum) to activate the configuration
Adjust the

focus

focus with the

precision

main dial while looking through the eyepieces until the image is perfectly sharp

Tip
Once calibrated, the focus is typically found at Z = 1.7 mm for a microscope slide. The Z position can be viewed on the microscope touch screen under Home > Z-Position, as well as in Zen within the Focus tab, located on the right side of the screen.

In the Locate tab, select Off to turn off the illumination

UI Expand

title	Seconday focus

Warning
Perform the initial focus using the safest objective before switching to higher-magnification objectives.

In the Locate tab, select Off to turn the illumination off

Your sample is ready for acquisition!

There are two (

UI Expand

title	Focusing with air objectives

After performing the initial focus, on the microscope touch screen:

Press Home>Microscope>Control>Objectives
Press 10x, 20x, 40x (0.95) to select the desired objective

Info
The 40× (0.95) Air objective is the best air objective because it has the highest number of optical corrections (Plan Apochromat) and the largest numerical aperture (0.95), but it has a smaller field of view. The 20×(0.8) objective offers the best compromise between resolution and field of view.

Warning
There are two (

UI Expand

title	Focusing with oil objectives

After performing the first focus, on the microscope touch screen:

Press Home>Microscope>Turret>Objectives

Press 63x Oil, 40x Oil to select the desired objective. The microscope will automatically lower the stage so that the sample is accessible.

Info

The 40x and 63x oil objectives provide the same spatial resolution because they have the same numerical aperture (1.4).
The 40x oil objective offers a larger field of view and transmits light slightly better beyond 700nm.
The 63x oil objective transmits light slightly better in the visible spectrum (440-710 nm) and has a better Strehl ratio (90%). It is particularly suited for super-resolution imaging, but its field of view is smaller.

Note

2) 40x objectives, make sure you select the 40x

Oil

Place a single drop of oil on the objective

Press Done. The microscope will automatically return the objective to its original position

Air (0.95)

In Zen:

In

the

the Locate tab, select BF or the desired fluorescence (DAPI, GFP

,

or mPlum) to activate the configuration
Adjust the focus with the precision dial while looking through the eyepieces

until the

until the image is perfectly sharp
In the Locate tab,

select

select Off to turn off the illumination

off

Your sample is ready for acquisition!

UI Expand

title

Storage management

Files can be saved temporarily (during acquisition) on the local C: drive (desktop)
At the end of each session, copy your data to your external drive and delete it from the local C: drive
You can store your files on the D: drive (Data Storage). If you do, please create a folder per laboratory using the principal investigator last name. Within, create one folder per user (Firstname_Lastname).

Note
In any case, your files should be removed from the C: drive.

UI Expand

title	Shutdown

Save your data

Close Zen

Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive

If used, clean oil lenses with lens cleaner and paper

Select the 5x objective and press load position to place the objectives in a safe position

Turn off the laser key (#4) in the rack below the microscope

Turn off theComponents (#3) and System (#2) switches in the rack below the microscope

Turn off the computer

Cover the microscope

Note

title	Important Reminders

Take back your samples including ones in the microscope
Leave the microscope and the working area clean

Tabs Page

id	Log
title	Log

UI Expand

title	To do

Quality control for Illumination, Liquid light guide and filters quality.

UI Expand

title	2024-09-19 Joystick replacement

Joystick replaced

UI Expand

title	2024-09-03 Airyscan upgrade

Installation Airyscan upgrade. New workstation. New detector. New casing.

UI Expand

title	2024-07-08 Joystick issue

Issue when the joystick is at the rest position. If it is slightly to the left, the stage will move while the image is acquired. Temporary fix: Make sure the joystick is slightly to the right when it is resting.

UI Expand

title	2024-02-14 Added to wiki

User guide added to Wiki French and english version

UI Expand

title	2021-10-20

Zen 2.6 updated hotfix 12
Microsoft Windows updated

UI Expand

title	2021-09-27

Added to wiki

Tabs Page

id	Technical Datasheet
title	Technical Datasheet

Stand

Zeiss AxioObserver LSM900 Serial: 2633000272
Manual Field diaphragm for transmitted light
Manual polarizer
Left imaging port with LSM900 confocal
Manual Aperture diaphragm
Manual Fluorescence field diaphragm
6x motorized nosepiece
6x Motorized reflector changer
3x Motorized sideport turret (100% Visible, 100% Left (confocal), 100% right (empty)
TL Motorized shutter
RL Motorized shutter

Light sources

Transmitted LED light
X-Cite 120LED mini Serial XT120LM-0279 RS232 COM Port 6
Laser URGB 400102-9300-000 Serial 2631000466 Toptica iChrome-ZLE-4_40407 v3.1 Aug 2016

Condenser

Manual condenser
Condenser Lens NA 0.55 WD 26mm
Manual polarizer
Filter turret 6 positions manual
1. H Empty
2. Ph1
3. Ph2
4. Ph3
5. DIC II #426702
6. DIC III #426706

Objectives

5x/0.15 Ph1 Air WD 5.6 N-AchroPlan 420931-9911-000
10x/0.25 Ph1 WD 6.0 N-AchroPlan 420941-9911-000
20x/0.80 Air WD 0.61 Plan-Apochromat 420650-9901-000
40x/0.95 Air WD 0.25 Plan-Apochromat 420660-9970-000 Variable coverslip 0.13-0.21
40x/1.4 Oil WD 0.13 Plan-Apochromat 420762-9900-000
63x/1.40 Oil WD 0.19 Plan Apochromat 420782-9900-799

Stage

Motorized stage Marzhauser Scan IM 130x100 Serial 14032630
Remote control joystick Marzhauser 2-Schsen-Joystick CZ Serial 2420142128 Article 90-76-200-0820 Zeiss Serial 432903-9011-000
Inserts
- Slide combo
- 6-well plate
- 35 mm dish
- Multi-well plat

Filters

6-Position motorized Filter Turret 424947

GFP Zeiss Filter Set 38 cube 424931 000000-1031-346 BP 470/40 450-490 FT 495 BP525/50 500-550
DAPI Zeiss Filter Set 49 cube 424931 489064-0000-000 G365 FT 395 BP 445/50 335-383 395 420-470
mPlum Zeiss Filter Set 64 HE cube 424931 489064-0000-000 BP587/25 FT605 BP647/70 574-599 605 612-682
DIC Analyzer Zeiss 424937-9901
Empty
Empty

Scanner

LSM900 Scan head

8x Motorized Filter wheel 1

Empty
SP 470 000000-2090-296 410-470 93% 480-750 0.001%
SP 545 000000-2090-297 410-546 93% 557-750 0.001%
SP 620 000000-2090-298 410-617 93% 630-750 0.001%
Empty
Empty
Empty
Empty

8x Motorized Filter wheel 2

Empty
LBF 640 0000000-2090-299 410-617 93% 630-644 0.001%
LP 575 0000000-2090-294 576-750 93% 410-565 0.001%
LP 655 0000000-2090-295 656-750 93% 395-643 0.001%
SP 620 000000-2090-298 410-617 93% 630-750 0.001%
Empty
Empty
Empty

Main Beam splitter

MBS 405+488+561+640 T10/R90

400102-9600-000

Transmission

420-471 93%
502-546 93%
575-618 93%
656-800 93%
631-642 10%

Reflection

399-410 99%
481-492 99%
558-564 99%
631-642 90%

Detector

2 GaASp PMT
1 Airyscan 2 63x Serial 2657000116
1 transmitted ESID Motorized Left TL ESID LED, Right ESID Detector

Workstation

HP Z2 G9 Serial CZC4027PF7 829W6EC#ABB
I155440-CIB
Motherboard HP 895C
BIOS version 2024-09-03
1 x Intel Core i7-12700K 3.6 GHz
RAM 128GB DDR5 4 x 32GB no ECC
OS 500 GB NVMe 6 GB/s
7 TB HD Data Storage 213 MB/s
Nvidia RTX A4000 16 GB GDDR6
Monitor HP Z32x
Software Zen 3.10 SN=1122911743-424077 HASP=110522193

Incubation

Consumables

Focusing with oil objectives

After performing the initial focus, on the microscope touch screen:

Press Home>Microscope>Turret>Objectives
Press 40x Oil (1.4) or 63x Oil (1.4)to select the desired objective. The microscope will automatically lower the stage so that the sample becomes accessible.

Info

The 40× and 63× oil objectives provide the same spatial resolution because they share the same numerical aperture (1.4).
The 40× oil objective offers a larger field of view and transmits light slightly better beyond 700 nm.
The 63× oil objective transmits light slightly better within the visible spectrum (440–710 nm) and has a higher Strehl ratio (90%). It is particularly well suited for super-resolution imaging, although its field of view is smaller.

Warning
There are two (2) 40x objectives, make sure you select the 40x Oil (1.40)

Place a single drop of oil on the objective
Press Done. The microscope will automatically return the objective to its original position

In Zen :

In the Locate tab, select BF or the desired fluorescence (DAPI, GFP or mPlum) to activate the configuration
Adjust the focus with the precision dial while looking through the eyepieces until the image is perfectly sharp
In the Locate tab, select Off to turn off the illumination

Your sample is ready for acquisition!

UI Expand

title	Storage management

Files can be saved temporarily (during acquisition) on the local C: drive (desktop)
At the end of each session, copy your data to your external drive and delete it from the local C: drive
You can store your files on the D: drive (Data Storage). If you do, please create a folder per laboratory using the principal investigator last name. Within, create one folder per user (Firstname_Lastname).

Note
In any case, your files should be removed from the C: drive.

UI Expand

title	Shutdown

Save your data
Close Zen
Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
If used, clean oil objectives with lens cleaner and paper
Select the 5x objective and press load position to place the objectives in a safe position
Turn off the laser key (#4) in the rack below the microscope
Turn off theComponents (#3) and System (#2) switches in the rack below the microscope
Turn off the computer
Cover the instrument with the protective dust cover

Note
Take back your samples including ones in the microscope Leave the microscope and the working area clean

Tabs Page

id	Log
title	Log

Log

UI Expand

title	To do

Quality control for Illumination, Liquid light guide and filters quality.
Revise Technical Datasheet

UI Expand

title	2025-10-09 20x and 40x Air objectives dirty

20x/0.8 and 40x/0.95 with immersion oil on it. Cleaning objectives.
Added Troubleshooting

UI Expand

title	2024-09-19 Joystick replacement

Joystick replaced

UI Expand

title	2024-09-03 Airyscan upgrade

Installation Airyscan upgrade. New workstation. New detector. New casing.

UI Expand

title	2024-07-08 Joystick issue

Issue when the joystick is at the rest position. If it is slightly to the left, the stage will move while the image is acquired. Temporary fix: Make sure the joystick is slightly to the right when it is resting.

UI Expand

title	2024-02-14 Added to wiki

User guide added to Wiki French and english version

UI Expand

title	2021-10-20

Zen 2.6 updated hotfix 12
Microsoft Windows updated

UI Expand

title	2021-09-27

Added to wiki

Tabs Page

id	Technical Datasheet
title	Technical Datasheet

Technical datasheet

Stand

Zeiss AxioObserver LSM800 System ID: 2633000272
Serial 3851002662 431007-9902-000
Manual Field diaphragm for transmitted light
Manual polarizer
Left imaging port Confocal
Manual Aperture diaphragm
Manual Fluorescence field diaphragm
6x motorized nosepiece
6x Motorized reflector changer
3x Motorized sideport turret (100% Visible, 100% Left (confocal), 100% right (empty)
TL Motorized shutter
RL Motorized shutter

Light sources

Transmitted LED light with ESID 423053-9071
X-Cite 120LED mini Serial XT120LM Serial XT120LM-0279 RS232 COM Port 6
Laser URGB 400102-9300-000 Serial 2631000466 Toptica iChrome-ZLE-4_40407 v3.1 Aug 2016

Condenser

Manual condenser # 424242
Condenser Lens NA 0.55 WD 26mm
Manual polarizer
Filter turret 6 positions manual
1. H Empty
2. Ph1
3. Ph2
4. Ph3
5. DIC II #426702
6. DIC III #426706

Objectives

5x/0.15 Ph1 Air WD 5.6 N-AchroPlan 420931-9911-000
10x/0.25 Ph1 WD 6.0 N-AchroPlan 420941-9911-000
20x/0.80 Air WD 0.61 Plan-Apochromat 420650-9901-000
40x/0.95 Air WD 0.25 Plan-Apochromat 420660-9970-000 Variable coverslip 0.13-0.21
40x/1.4 Oil WD 0.13 Plan-Apochromat 420762-9900-000
63x/1.40 Oil WD 0.19 Plan Apochromat 420782-9900-799

Stage

Motorized stage Marzhauser Scan IM 130x100 Serial 14032630
Remote control joystick Marzhauser 2-Schsen-Joystick CZ Serial 2420142128 Article 90-76-200-0820 Zeiss Serial 432903-9011-000
Inserts
- Slide combo
- Multi-well plate

Filters

6-Position motorized Filter Turret ##424947

GFP Zeiss Filter Set 38 cube 424931 000000-1031-346
DAPI Zeiss Filter Set 49 cube 424931 489064-0000-000 (in MTB 488049-0000-000)
mPlum Zeiss Filter Set 64 HE cube 424931 489064-0000-000
DIC Analyzer Zeiss 424937-9901
Empty
Empty

Scanner

LSM 800 GaAsP-PMT 400102-9000-00000 confocal 2633000272 (in MTB LSM900 Scanhead)

8x Motorized Filter wheel 1

Empty
SP 470 000000-2090-296 410-470 93% 480-750 0.001%
SP 545 000000-2090-297 410-546 93% 557-750 0.001%
SP 620 000000-2090-298 410-617 93% 630-750 0.001%
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8x Motorized Filter wheel 2

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LBF 640 0000000-2090-299 410-617 93% 630-644 0.001%
LP 575 0000000-2090-294 576-750 93% 410-565 0.001%
LP 655 0000000-2090-295 656-750 93% 395-643 0.001%
SP 620 000000-2090-298 410-617 93% 630-750 0.001%
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Main Beam splitter : MBS 405+488+561+640 T10/R90 400102-9600-000

Transmission

420-471 93%
502-546 93%
575-618 93%
656-800 93%
631-642 10%

Reflection

399-410 99%
481-492 99%
558-564 99%
631-642 90%

Detector

2 GaASp PMT
1 Airyscan 2 63x Serial 2657000116 2263-682
1 transmitted ESID Motorized Left TL ESID LED, Right ESID Detector

Workstation

HP Z2 G9 Serial CZC4027PF7 829W6EC#ABB
I155440-CIB
Motherboard HP 895C
BIOS version 03.04.08 Rev.A 2025-07-02
1 x Intel Core i7-12700K 3.6 GHz
RAM 128GB DDR5 4 x 32GB no ECC
OS 500 GB NVMe 6 GB/s
Data Storage 14 TB (2 x 7 TB) HD 14 TB (2 x 7 TB) HD 213 MB/s
Nvidia RTX A4000 16 GB GDDR6
Monitor HP Z32x CNC61804QR 3840 x 2160 60 Hz CNC61804QR 3840 x 2160 60 Hz
Software Zen 3.10 SN=1122911743-424077 HASP=110522193
Zen Module Arivis Cloud Basic, Arivis Cloud Advanced, Colocalization, Data Storage, Direct Processing, Manual extended Focus, Measurements Multi-Channel. Panorama, Time Series, Advance Processing, Airyscan, Airyscan 2 Basic, Ariscan Hoiunt Deconvolution Exteneded Focus, HDR Confocal Basic, Image Analysis, Sotfware Autofocus, Tiles and Positions, Z Stack

Incubation

Pecon stage top incubation

Consumables

CO₂ Tank
N₂ Tank
Oil
Lens Cleaner

Manuals

XCite_120LEDmini_User Manual.pdf

The best way to solve a problem in Microscopy is to follow the light path. You will find in the Light path tab of this page, the diagrams which will allow you to follow the light all along its path through the microscope.

Open the light path file
Starting from the light source and moving towards the detector, verify that there is indeed light after each component of the microscope

FAQ

Tabs Page

title	Troubleshooting & FAQ

Troubleshooting

UI Expand

title	I don't see any fluorescence!

Technical support is free and unlimited. Contact us !

UI Expand

title	My image is blurry

This can happen when objectives are dirty. this is especially true for the 20x/0.8 and 40x/0.95 which have a short working distance. If not careful immersion oil can make them dirty. If your image seems blurry with one of these objective please contact us and we will clean it for you !

Image Added

FAQ

UI Expand

title	Can I use this microscope to perform timelapse experiments?

Yes, but... This microscope has an incubation module to maintain temperature, humidity and atmosphere. Yet, it does NOT have a module which can maintain focus throughout time. Therefore, it is possible to loose the focus over long period. You can always do a software auto-focus at different time but be aware of photo-toxicity if you are using fluorescence.

UI Expand

title	What is Extended Depth of Focus?

Extended Focus is a method to flatten a Z-stack by keeping only the relevant information.

In Zen:

Select the Processing Tab
Select the Extended Depth of Focus Method
Click Apply
Wait until the processing is finished
Save the processed image

Image AddedImage AddedImage Added

Tabs Page

id	FAQ
title	Troubleshooting & FAQ

Troubleshooting

UI Expand

title	I don't see any fluorescence!

UI Expand

title	Can I use this microscope to observe cells in culture?

Yes. It This is an a inverted microscope designed for observing specimens in culture. The objectives are optimized for viewing through glass-bottom to look at sample in a dish or a multi-well plates. It is also possible to observe samples between a slide and coverslip (with a thickness of 0.17mm)plate. For long timelapse, be aware of photo-toxicity.

Include Page

	Plateformes:_Plat-foot-en
	Plateformes:_Plat-foot-en

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Old Version 40

New Version Current

Key

Zeiss LSM-900 confocal Airyscan microscope

Applications

Description

Light sources

Objectives

Filters

Detectors

User Guide

Stand

Light sources

Condenser

Objectives

Stage

Filters

Scanner

Detector

Workstation

Incubation

Consumables

Log

Technical datasheet

Stand

Light sources

Condenser

Objectives

Stage

Filters

Scanner

Detector

Workstation

Incubation

Consumables

Manuals

Troubleshooting

FAQ

Troubleshooting

FAQ