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id	Instrument Tabs
direction	horizontal

Tabs Page

id	Description
title	Description

Light sources

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

Expand

title	Complete specifications

Emission (nm)	Nominal 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 (mW)	Measured Power (mW)
DAPI	365
GFP	470
mPlum	587

XCite_120LEDmini_Datasheet.pdf

XCite_120LEDmini_User Manual.pdf

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	ID	Magnification	Numerical aperture	Immersion	Type	Working distance (mm)	Transmittance (% [nm])	Applications	Coverglass thickness (mm)
1	5x/0.15 Air	Zeiss	5x/0.15 Ph1 N-AchroPlan	420931-9911-000	5x	0.15	Air	N-AchroPlan	12.0	Not Available	BF, PhC, Fluo	0.17
2	10x/0.25 Air	Zeiss	10x/0.25 Ph1 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 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 Plan-Apochromat	420660-9970-000	40x	0.95	Air	Plan Apochromat	0.25	>80% [410-820]	BF, DIC, Fluo	0.13-0.21
5	40x/1.4 Oil	Zeiss	40x/1.4 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 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

Filters

GFP
DAPI
mPlum
DIC Analyzer
Empty
Empty

Expand

title	Complete specifications

Position	Name	Brand	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	-	-	-	-	-	-	-
6	-	-	-	-	-	-	-

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

Zeiss

Expand

title	Complete specifications

Zeiss_LSM 800_Brochure.pdf

Zeiss_Airyscan_Brochure.pdf

Tabs Page

id	User Guide
title	User Guide

UI Expand

expanded	true
title	Startup

If not already done, turn on the computer (#1) and log in to Windows using your UdeM credentials
Remove the dust cover from the microscope
If incubation is required, turn on the incubation power bar (#2) on the desk near the computer and open the CO₂ cylinder (#2B) near the sink
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 configuration into the software. See the First Use section below.
Start Zen

UI Expand

title	First Use

When using the instrument for the first time, it is necessary to import the microscope configuration into the software. This procedure is usually carried out during the training session. However, it can also be used to reset the software if it does not display correctly, for example. Running this procedure will erase all your experiment protocols and reset the software to its original settings (ask for support if you are not sure).

If Zen is open, close it and wait until it has completely shut down (this may take up to 30 seconds)
On the Desktop, open the Softwares folder
Double-click Zen Settings for

LSM900

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

message

message Settings for Zen have been imported successfully appears, click OK to close it
You can now open Zen

UI Expand

title	Loading samples

During this procedure, you will set :

Set the microscope to a safe configuration

, perform

Perform a calibration

, load

Load your sample

,

Find and adjust the focus

. Once completed, your sample will be ready for acquisition.

If not already done, select the lowest-magnification objective

:

. On

the

the microscope touch

screen, Home

screen Home > Microscope > Control > Objectives > 5x
In Zen

:Click

, 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. Performing this calibration will significantly reduce the time needed to locate and focus on your sample.

UI Expand

title	Calibration with the software

note

Info

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.

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, slightly adjust the focus upward to clear the Lower Z Limit Reached message displayed on the 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 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 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

On the microscope touch screen:

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

touch screen
Navigate to Home > Microscope > XYZ > Position > XY-Position > Set Zero > Auto to perform a stage

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

complete

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

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

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 Initial focus

Warning

title	Important

Make sure to calibrate the focus before performing the first focusEnsure 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,

press Home>Microscope>Turret>

Objectives>5x

to

select the

5x

objective

lowest-magnification objective Home > Microscope > Control > Objectives > 5x

Info
The

5x

5× objective is

the safest because it has the longest

the safest to use due to its long working distance (

12mm

12 mm). The sample will appear

perfectly

in sharp

long

focus well before the

lens

objective approaches it. It is recommended

to always first

to always focus

with

using the safest

lens

objectives first.

The

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

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.If not done already, press Home>

Load Position

to lower the objective to the lowest position and press

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

touch screen
Place the test slide on the microscope stage with the coverslip

toward

facing the objective
Note
title Important

Always use the

Using a test slide

to perform the first focus

will significantly reduce the time required to set up the instrument.
If necessary,

move

adjust the stage

so

to ensure that the sample is

centered on

centred under the objective

On the computer:

Open Zen

In Zen:

In

the

the Locate tab, select BF or the desired

fluorescence

fluorescence (DAPI, GFP

,

or mPlum) to activate the configuration
Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp

note

Info
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

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

title	Important

First focus with the safest objective before selecting another lens and continuing with secondary focusPerform the initial focus using the safest objective before switching to higher-magnification objectives.

UI Expand

title	Focusing with air objectives

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

Press Home>Microscope>Control>Objectives

,

press
Press
10x, 20x

or

40x

to

, 40x-0.95 Air to select the desired objective

Info
The

40x

40×-0.95 Air objective is the best

Air

air objective because it has the

greatest

highest number of optical corrections (Plan Apochromat) and the largest numerical aperture (0.95), but it has a smaller field of view.
The

20x

20×/0.8 objective offers the best compromise between

Resolution

resolution and

Field

field of

View

view.

note

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

focus with the precision dial while looking through the eyepieces 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	Focusing with oil objectives

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

Press Home>Microscope>Turret>Objectives
Press

63x Oil

,

40x Oil

40x Oil (1.4) or 63x Oil (1.4)to select the desired objective.The microscope will automatically

lower the
lower the stage so that the sample
is
becomes accessible.
Info
The
40x
40× and
63x
63× oil objectives provide the same spatial resolution because they
have
share the same numerical aperture (1.4).
The
40x
40× oil objective offers a larger field of view and transmits light slightly better beyond
700nm
700 nm.
The
63x
63× oil objective transmits light slightly better
in
within the visible spectrum (
440-710
440–710 nm) and has a
better
higher Strehl ratio (90%). It is particularly well suited for super-resolution imaging,
but
although its field of view is smaller.
note
Warning
There are two (2) 40x objectives, make sure you select the Oil 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
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

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

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

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

the computer
Cover

the microscope

the instrument with the protective dust cover

Note

title	Important RemindersReminder

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.
Revise Technical Datasheet

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 System ID: 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
- Multi-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 445/50 335-383 395 420-470-000
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 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

Pecon stage top incubation

Consumables

CO₂ Tank
N₂ Tank
Oil
Lens Cleaner

Tabs Page

id	FAQ
title	Troubleshooting & FAQ

Troubleshooting

UI Expand

title	I don't see any fluorescence!

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

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 in Microscopy is to follow the light all along its path through the microscope.

Open the light path file

.Check along the way that light is present. On a confocal system you may open the pinhole to see the full depth. This will help to find your focus.

FAQ

UI Expand

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

Yes. It is an inverted microscope designed for observing specimens in culture. The objectives are optimized for viewing through glass-bottom multi-well plates. It is also possible to observe samples between a slide and coverslip (with a thickness of 0.17mm).

Include Page

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

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Versions Compared

Old Version 43

New Version 44

Key

Zeiss LSM-900 confocal Airyscan microscope

Light sources

Objectives

Filters

Detectors

Stand

Light sources

Condenser

Objectives

Stage

Filters

Scanner

Detector

Workstation

Incubation

Consumables

Troubleshooting

FAQ

Space shortcuts

Page tree

Page History

Versions Compared

Old Version 43

New Version 44

Key

Zeiss LSM-900 confocal Airyscan microscope

Light sources

Objectives

Filters

Detectors

Stand

Light sources

Condenser

Objectives

Stage

Filters

Scanner

Detector

Workstation

Incubation

Consumables

Troubleshooting

FAQ