Tabs Container

id	Instrument Tabs
title	Zeiss Axio-Observer Z1
direction	horizontal

Tabs Page

id	Description
title	Description

Zeiss Axio-Observer Z1 inverted microscope

Roger Gaudry Building, Room R-421

Access upon request to the platform manager. Consult the

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Serial Camera 1 22 12 5537 r3.1 426509-9901-000

Identifiant système 1024979772.

Applications
- Bright-field
- Phase contrast
- Fluorescence
Light sources
- LED lamp for transmitted light
- X-Cite 120Q 100 W (350~600nm) for fluorescence

Développer

title	X-Cite complete specifications

Emission peak (nm)	Power (mW)
334	7
365	45
405	34
436	43
546	37
579	26

X-Cite 120Q Brochure (pdf)
X-Cite 120Q quick start guide (pdf)
X-Cite 120Q user guide (pdf)
Comparison between mercury and X-Cite emission spectra (Source)

Objectives
1. 2.5x/0.085 Air WD 8.8
2. Empty
3. 10x/0.25 Air Ph1 WD 6.5
4. Empty
5. 20x/0.5 Air Ph2 WD 2.0
6. 40x/0.95 Air WD 0.25

Développer

title	Objectives complete specifications

Position	Name	Brand	Full name	ID	Magnification	Numerical Aperture	Immersion	Type	Working distance (mm)	Transmittance (% [nm])	Technique	Cover glass thickness (mm)
1	20x/0.5 Air	Zeiss	20x/0.50 Ph2 EC Plan-Neofluar M27	420351-9910	20x	2.0	Air	Plan Neofluar	2.0	Not Available	BF, PhC, Fluo	0.17
2	Empty
3	40x/0.95	Zeiss	40x/0.95 Plan-Apochromat Corr M27	420660-9970	40x	0.95	Air	Plan ApoChromat	0.25	>80% [400-840]	BF, Fluo	0.13 - 0.21 Correction ring
4	Empty
5	2.5x/0.085 Air	Zeiss	2.5x/0.085 EC Plan-Neofluar M27	420320-9902	2.5x	0.085	Air	Plan Neofluar	8.8	>95% [400-750]	BF, Fluo	0.17
6	10x/0.25 Air	Zeiss	10x/0.25 Ph1 N-Achroplan M27	420941-9911	10x	0.25	Air	AchroPlan	6.5	Not available	BF, PhC, Fluo	0.17

Filter cubes
1. DAPI
2. GFP
3. Rhodamine
4. DHE (dihydroethidium)
5. Cy5

Développer

title	Filters complete specifications

Position	Name	Brand	ID	Excitation filter	Dichroic mirror	Emission filter	Comments
1	DAPI Filter Set 49	Zeiss	488049-9901	365/50 [325-375]	395LP	445/50 [420-470]
2	GFP Filter Set 13	Zeiss	488013-0000	470/20 [460-480]	495LP	517/25 [505-530]
3	Rhodamine Filter Set 43	Zeiss	000000-1114-101	545/25 [533-567]	570LP	605/70 [570-640]
4	DHE	Custom	Custom	500/50 [475-525]	540LP	580/20 [570-590]	Undefined specifications Best guess values
5	Cy5 Filter Set 50	Zeiss	488050-9901	640/30 [625-655]	660LP	690/50 [665-715]
6	Empty

Détector
- Zeiss AxioCam MR R3 CCD Camera 1388 x 1040 pixels, 12-bit, 13 images/s at full resolution, detector size 8.9 mm x 6.7 mm

Tabs Page

id	User Guide
title	User Guide

UI Expand

expanded	true
title	Start-up

Turn on the computer (#1)
Turn on the microscope power bar (#2)
If incubation is required, turn on the Okolab incubation module (#3A) and the Lauda water-bath (#3B) and open the CO₂ (#3C) and N₂ (#3D) tanks
Avertissement
Make sure the humidifier and the water bath are clean and properly filled with distilled water.
Log in Windows using your UdM credentials
Start-up NIS-Elements

Info
The first time you use the instrument, you need to import the microscope settings into the software. To do this follow the instructions Software setup.

UI Expand

title	Shutdown

Save your data
Close NIS-Elements
Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
Turn off the computer
If oil objectives were used, clean it with lens cleaner and lens paper (not Kimwipes)
If incubation was used, turn off the Okolab incubation module (#3A) and Lauda water-bath (#3B) and close the CO₂ (#3C) and N₂ (#3D) tanks
Turn off the microscope power bar (#2)
Cover the microscope

Remarque

title	Important Reminders

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

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).

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

UI Expand

title	Software setup

The first time you use the instrument, you need to import the microscope settings into the software. You will usually do this during the training session.
This procedure can also be performed if something is not working properly and if you want to reset the software to its original settings.

Remarque
This process will delete all experiment protocols and reset the software to the original settings for this specific microscope.

If open, close NIS-Elements and wait until it is completely closed (up to 30 seconds)
On your Desktop open the Softwares folder
Open NIS Settings Utility
Click on the Import tab
Click on Browse
Navigate to your Desktop
Select the file Nikon-Ti2 Settings.bin
Click Select
Select all items
Click Import
Click OK
Close the NIS Settings
You can now reopen NIS-Elements

Tabs Page

id	Lightpath
title	Lightpath

The following schematics depict the light path for transmitted (bright-field and Phase Contrast) and reflected (fluorescence) lights.

Nikon Ti2 Zeiss Axio-Observer Z1 Lightpath (pdf)

Tabs Page

id	Manuals
title	Manuals

Available manuals

Lumencor SpectraX Manual Zen Quick Guide (pdf)
Lumencor SpectraX Filter recommandation (pdf)
Lumencor SpectraX Brochure (pdf)
Nikon Ti2 Brochure (pdf)
Hamamatsu ORCA Flash 4.0 V2 Instruction Manual AxioCam MR Reference Guide (pdf)
Hamamatsu Orca Flash 4.0 V2 C11440-22CU Technical Note (pdf)
Nikon NIS-Elements AR Manual (pdf)

Tabs Page

id	Log
title	Log

UI Expand

title	To do

Nothing

UI Expand

title	2022-03-17

Added complete description

UI Expand

title	2021-09-27

Added to wiki

Tabs Page

id	Technical Datasheet
title	Technical Datasheet

Stand

Nikon Ti2-E Zeiss Axio-Observer Z1 inverted Serial 540156 System 170110-Sys-006287
System ID: 1024979772
Camera adapter Model 60N-C, 1", 1x, Model: 426114

Light sources

Transmitted LED light
- ND32 filter
- IR filter
- Manual Polarizer
- TBD Filters
X-Cite 120Q Serial: TBDLumencor SpectraX 6-NII-SE Serial 9409

Condenser

Motorized condenser Ti2-C-TC-E Serial 519097
Lens LWD NA 0.52
Filter turret 7 motorized positions
1. Empty
2. Empty
3. Ph1
4. Ph3
5. Shutter
6. Empty
7. DIC N1

Objectives

20x/0.5 Air Ph1 WD 2.1
60x/1.4 Oil DIC WD 0.13
100x/1.45 Oil Ph3 WD 0.13
100x/1.45 Oil DIC WD 0.13
4x/0.2 Air WD 20
20x/0.75 Air DIC WD 1.0

Stage

Motorized stage Ti2 SHU compatible Serial 127808
Remote control joystick Ti2-S-JS Serial 127976
Inserts
- Multi-well plate Ti2-S-HW with tilt adjustment (no incubation)
- Combo slide 3cm dish Ti2-S-HU with tilt adjustment (no incubation)
- Okolab H101-CellASIC Frame with perfusion ports
  - 1 x 35mm petri dish 1x35-M + cover
  - 2 Chamber Slide 2xGS-M+ cover
  - 1 Multi-well for oil objectives MW-OIL
  - 6-well plate 6MW+ cover
  - 1 CellASIC + cover

Filters

DAPI Cube Ex 383-408 DAPI-U DM 425 BA 435-485
GFP Cube Semrock 96372 M349727 17
Cy5 Cube Semrock 96376 M351081 8
77074160 Custom Quad C182279 Polychroic and quad bandpass emitter for use with the following single bandpass filters: ET395/25x, ET470/24x, ET550/15x, ET640/30x
DIC Analyser Ti2-C-DICACL
C197767 7707\4656 CFP\YFP\mCherry XT

Detector

Hamamatsu ORCA Flash V2 C11440-22CU CMOS Monochrome Camera 2048 x 2048 pixels, 16-bit, 30fps at full frame Serial 101081

Workstation

Manual condenser Product number: TBD, Serial: TBD
Lens NA 0.35 WD 70 mm Part Number: 424241
Filter turret 6 positions manual
1. H
2. Ph0
3. Ph1
4. Ph2
5. DIC
6. DUC

Objectives

2.5x/0.085 Air WD 8.8
Empty
10x/0.25 Air Ph1 WD 6.5
Empty
20x/0.5 Air Ph2 WD 2.0
40x/0.95 Air WD 0.25

Stage

Motorized stage Marzhauser Sensotech, Part number 432903-9011-000, #14 07 132052; 90-76-200-0820
Remote control joystick
Inserts
- Slide combo
- 6-well plate
- 35 mm dish
- Multi-well plat

Filters

DAPI Filter Set 49
GFP Filter Set 13
Rhodamine Filter Set 43
DHE (dihydroethidium)
Cy5 Filter Set 50
Empty

Detector

Zeiss AxioCam MR R3 CCD Camera 1388 x 1040 pixels, 12-bit, 13 images/s at full resolution, detector size 8.9 mm x 6.7 mm. Model: r3.1 Part Number: 426509-9901-000. Serial: 1 22 12 5537

Workstation

Fujitsu Esprimo P920 E90+
Intel Core i5-4670 @ 3.4 GHz
RAM 32 GB DDR3 1600
HP Z440 Workstation
Intel Xeon E5-1620 v4 @ 3.5GHz
RAM 32 GB DDR4 2400 MHz ECC (4 x 8 GB)
OS 500 GB SSD 550 MB/s
4 2 TB HD Data Storage (2 x 2 1 TB spanned volume) 170 110 MB/s
Video Card nVidia GTX 1080 8GB Card AMD FirePro V4900 1 GB DDR5 dedicated memory
Monitor HP Z24i Monitor TBD display 24TBD' 1920x12001920 x 1200
Software NIS-Elements AR v5.02Zen Blue 2.0

Incubation

Okolab BoldLine Temperature unit Serial 284-1058 H101 T Unit BL
Okolab BoldLine CO₂/O₂ Unit 0-10/1-18 Serial 088-1102
Okolab OkoTouch Serial 118-224
Lauda water-bath Model Eco RE415 S LCK 4910 Serial LCK-4910-16-0006 Okolab 1322-1006 2017-05-30

Pecon incubation
TBD

Consumables

CO₂ Tank
N₂ Tank
Liquid Light Guide
100 W Mercury lamp

The liquid from the water bath enters the lead first via the red pipe
Then it goes through the lead circuitry to keep it warm
It exists via the unlabeled tube and enters the incubation chamber main body
It goes through the circuitry of the main body and exits via the green labelled tube

One must maintain a decent amount of liquid in the Lauda water bath to avoid bubble formation in the circuitry

Because the circuitry inside the top lead and the incubation chamber main body is thin it can get clogged. The procedure above can solve this issue.

This happens when the mixed-gas humidifier is overfilled. Bubbles created by the gas going through the humidifier can bring liquid into the gas feed line.

Turn off the Okolab module and the water bath
Remove your sample and store it properly
Dry the incubation chamber with a clean tissue
Carefully remove the cap of the humidifier glass bottle

Tabs Page

id	FAQ
title	Troubleshooting & FAQ

Troubleshooting

This can happen when the liquid running through the chamber is not flowing properly.

Pause your experiment
Turn off the Okolab environment controller 3A and 3B
Disconnect the blue end of the connection pipe (at the junction with the spring shape objective warmer)
Place the open end into a dish to collect liquid
Turn the Lauda water bath back ON (3B)
The liquid should flow quite rapidly, if not proceed as follow
- Turn OFF the Lauda water bath (3B)
- Take the 20 mL syringe located inside the drawer labelled Tubing
- Connect it to the open end of the blue pipe
- Use the syringe to blow pressurized air into the pipes to clear it out
- Remove the syringe (and store it back into the Tubing drawer)
- Test if the liquid is now flowing properly by turning the Lauda water bath back ON (3B)
  - If not repeat the procedure
  - If so, turn OFF the Lauda water-bath (3B)
  - Reconnect the blue and green pipes together
  - Turn the Okolab environment controller 3A and 3B back ON

UI Expand

title	Chamber does not reach the desired temperature (or is very slow to warm up)

Avertissement
Be careful not to touch your sample when performing these actions as it may displace your current acqusition

Info

title	How the Okolab chamber works

UI Expand

title	Liquid forming inside the incubation chamber

Avertissement
Pay extra care when manipulating the humidifier bottle as it is made of glass and is very fragile

Remove distilled water from the humidifier

Info
Humidifier shouldn't be more than 2/3^rd filled

Close the humidifier by replacing the cap
Turn on the Okolab module and the water bath

UI Expand

title	Liquid forming inside the incubation chamber but the humidifier is not overfilled

This can happen during long experiments. The high humidity of the gas mixture condensates in the pipe between the humidifier and the incubation chamber.

Pause your experiment
Disconnect both ends of the yellow tube from the humidifier
Drain the tube from any liquid
Reconnect the yellow tube to the humidifier
You can use a syringe or gas pressure to blow out any liquid from the incubation chamber cover

Avertissement
Be careful not to touch your sample when performing this action

Wipe any liquid with a tissue
Reconnect the yellow tube to the incubation chamber

I don't see any fluorescence!

This microscope is motorized for most of its components, yet the X-Cite light source is manual. Ensure the X-Cite diaphragm (#4B) fully opened (high position).

On the X-Cite lamp
Turn the intensity diaphragm (#4B) up

FAQ

UI Expand

title	Can I use this microscope to look at cell in a dish?

Yes. This is an inverted microscope designed to look at specimen in a dish or a multi-well plate
The objectives are optimized to image through thin glass bottom multi-well plates
You may also image specimen mounted between a slide and a 0.17mm thick coverslip
For long timelapse, be aware of photo-toxicity

UI Expand

title	How can I warm up the incubation chamber faster?	Can I use this microscope to perform timelapse experiments?

Yes, but... This microscope has an incubation module to maintain temperature, humidity and gas. Yet it does not have a Definite focus which can maintain focus throughout time. Therefore, it is possible to loose the focus over long period.

You may use a trick to warmup the incubation chamber faster. Using this method. you should reach a stable temperature within 30 minutes.

Avertissement
Do NOT proceed with your sample but with a blank control (dish with distilled water for example)

Place your blank control in the incubation chamber
Immerge the tip of the sample temperature probe in the blank
Set the Okolab temperature Control Mode to Chamber (Settings>Temperature>Control Mode>Chamber>Save)
Set the Okolab temperature to 50°C (Home>Temperature>50°C>Set)
Check the temperature of the sample (Menu Magnifier>Sample Temperature). It should take between 10 to 15 minutes for the blank to reach 30°C.

Info
The Lauda water bath is faster to warm up water than to cool it down. Make sure to anticipate and not pass beyond the desired temperature. If your desired temperature is 37°C, you can stop the procedure when the blank has reached 30°C.

When the blank has reach the desired temperature

Set the Okolab temperature back to 37°C (Home>Temperature>37°C>Set)

Set the Okolab temperature Control Mode to Sample (Settings>Temperature>Control Mode>Sample>Save)

Wait 10 to 20 minutes until the temperature stabilizes

Then you can safely replace the blank with your sample

Tabs Container

id	Demo Image
title	Zeiss Axio-Observer Z1
direction	horizontal

Tabs Page

id	Demo Image
title	Demo Image

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Raccourcis espace

Arborescence des pages

Comparaison des versions

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Légende

Zeiss Axio-Observer Z1 inverted microscope

Stand

Light sources

Condenser

Objectives

Stage

Detector

Workstation

Objectives

Stage

Filters

Detector

Workstation

Incubation

Consumables

Troubleshooting

FAQ

Raccourcis espace

Arborescence des pages

Historique de la page

Comparaison des versions

Ancienne version 14

Nouvelle version 15

Légende

Zeiss Axio-Observer Z1 inverted microscope

Stand

Light sources

Condenser

Objectives

Stage

Detector

Workstation

Objectives

Stage

Filters

Detector

Workstation

Incubation

Consumables

Troubleshooting

FAQ