GI - Recent changes [en]

Nikon TIRF switch on

Jelle — Wed, 10 Jun 2026 09:12:38 GMT

reordered

← Older revision		Revision as of 09:12, 10 June 2026
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	6) '''Main camera''' (Prime BSI, to actually observe the sample through the objective lens)		6) '''Main camera''' (Prime BSI, to actually observe the sample through the objective lens)

			7) '''Computer''' (for observation and imaging by camera, otherwise you can only use the eyepieces)

	=== '''Optional elements''' ===		=== '''Optional elements''' ===
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	3) '''Humidity + CO2''' (for live-cell incubation)		3) '''Humidity + CO2''' (for live-cell incubation)

	~~7) '''Computer''' (for observation and imaging by camera, otherwise you can only use the eyepieces)~~


	'''-> When in doubt:''' Switch them all on		'''-> When in doubt:''' Switch them all on

Nikon TIRF widefield

Jelle — Wed, 10 Jun 2026 09:11:39 GMT

← Older revision		Revision as of 09:11, 10 June 2026
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	[[TIRF alignment guide]]		[[TIRF alignment guide]]

	How to switch on		[[Nikon TIRF switch on\|How to switch on]]
	== Current status ==		== Current status ==
	The current status of the microscope can be found [[Current microscope status#Light microscopes\|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].		The current status of the microscope can be found [[Current microscope status#Light microscopes\|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].

Nikon TIRF switch on

Jelle — Wed, 10 Jun 2026 09:11:11 GMT

completed the steps

← Older revision		Revision as of 09:11, 10 June 2026
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	[[File:TIRF switch on.png\|880x880px]]		[[File:TIRF switch on.png\|880x880px]]

			=== '''Required elements''' ===
			4) '''Controller''' (this operates the microscope)

	~~Required elements~~		5) '''Internal camera''' (Fi3, to inspect the objective back aperture to guarantee TIRF, software always requires this on)

	~~4: Controller~~ (~~this operates~~ the ~~microscope~~)		6) '''Main camera''' (Prime BSI, to actually observe the sample through the objective lens)

	~~5: Internal cam~~ (to ~~inspect the objective back aperture to guarantee~~ TIRF, ~~software always requires this on~~)		=== '''Optional elements''' ===
			1) '''Lasers''' (if you want to actually do TIRF, or use the specific laser wavelengths for widefield epifluorescence)

			2) '''Warming box''' (if you want to have the incubator box light available, and for if you want to do live-cell incubation)

			3) '''Humidity + CO2''' (for live-cell incubation)

	~~Optional elements~~		7) '''Computer''' (for observation and imaging by camera, otherwise you can only use the eyepieces)

	~~1: Lasers (if you want to do TIRF or use lasers for widefield)~~

	~~2: Warming box (if you want to have the box~~-~~light available or for live-cell incubation)~~		'''-> When in doubt:''' Switch them all on

	3: ~~CO2 and humidity (for live-cell incubation)~~

Nikon TIRF switch on

Jelle — Wed, 10 Jun 2026 08:03:35 GMT

dsf

New page

[[File:TIRF switch on.png|880x880px]]

Required elements

4: Controller (this operates the microscope)

5: Internal cam (to inspect the objective back aperture to guarantee TIRF, software always requires this on)

Optional elements

1: Lasers (if you want to do TIRF or use lasers for widefield)

2: Warming box (if you want to have the box-light available or for live-cell incubation)

3: CO2 and humidity (for live-cell incubation)

File:TIRF switch on.png

Jelle — Wed, 10 Jun 2026 08:00:52 GMT

Jelle uploaded File:TIRF switch on.png

New page

which components to switch on to switch on the TIRF microscope and in which order

Nikon TIRF widefield

Jelle — Wed, 10 Jun 2026 07:59:47 GMT

← Older revision		Revision as of 07:59, 10 June 2026
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	== Manuals and user guides ==		== Manuals and user guides ==
	[[TIRF alignment guide]]		[[TIRF alignment guide]]

			How to switch on
	== Current status ==		== Current status ==
	The current status of the microscope can be found [[Current microscope status#Light microscopes\|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].		The current status of the microscope can be found [[Current microscope status#Light microscopes\|here]] and on the [https://bookings.science.ru.nl/category/general-instrumentation-gi/gi-light-microscopy-image-analysis booking website].

Nikon sora introduction protocol

Jelle — Thu, 28 May 2026 15:40:07 GMT

← Older revision		Revision as of 15:40, 28 May 2026
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	* Two-camera option for capturing two fluorescent colors at the same time (dynamic processes)		* Two-camera option for capturing two fluorescent colors at the same time (dynamic processes)
	* Fluorescence Recovery After Photobleaching (FRAP) to study molecular diffusion times		* Fluorescence Recovery After Photobleaching (FRAP) to study molecular diffusion times



	[[Nikon sora switch on\|'''Switch-on procedure''']] (link)		[[Nikon sora switch on\|'''Switch-on procedure''']] (link)
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	'''Stage-top incubation system for live-cell imaging (switch on before starting a live cell experiment)'''		'''Stage-top incubation system for live-cell imaging (switch this on before starting a live cell experiment)'''

	* Component 2 is the "Warming box" and needs to be switched on as well as the "Heater" button on its front panel		* Component 2 is the "Warming box" and needs to be switched on as well as the "Heater" button on its front panel
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	* The "canal" should be filled with MQ water using the attached tubing - the tubing sticks out of the front of the microscope		* The "canal" should be filled with MQ water using the attached tubing - the tubing sticks out of the front of the microscope
	* Unclip the tubing clip, attach a syringe with MQ water fill stage-top incubator "canal" with MQ water		* Unclip the tubing clip, attach a syringe with MQ water fill stage-top incubator "canal" with MQ water
	* Clip the tubing clip again, remove the syringe, and cover the canal with the plastic frame. It is ready to use		* Clip the tubing clip again, remove the syringe, and cover the canal with the plastic frame. It is ready to use<br />
			'''First manual operations (moving things around)'''


	'''First manual operations'''

	* Operate the lens switcher at the front of the microscope and select the 100X / Oil lens.		* Operate the lens switcher at the front of the microscope and select the 100X / Oil lens.
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	* Center the stage above the objective.		* Center the stage above the objective.
	* Operate the focus knob on the side of the joystick to see the objective move up and down (also may have to switch the movement speed to fast).		* Operate the focus knob on the side of the joystick to see the objective move up and down (also may have to switch the movement speed to fast).
	* Lower the lens as far as possible down to prepare for placing the sample.		* Lower the lens as far as possible down to prepare for placing the sample.<br />
			'''First brightfield observation (finding the sample)'''


	'''First brightfield observation'''

	* Mount a demo sample (or user sample) in the appropriate sample holder without placing it in the microscope yet		* Mount a demo sample (or user sample) in the appropriate sample holder without placing it in the microscope yet
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	* Go to the computer and make sure everyone can see the screen		* Go to the computer and make sure everyone can see the screen
	* Point out that the software looks complicated but we will discuss the essential parts to understand them		* Point out that the software looks complicated but we will discuss the essential parts to understand them
	* ~~Roughly describe~~ that there are modalities (Eye-observation, Epifluorescence with camera, Spinning-disc modalities).		* Point out that there are modalities and buttons to switch to them (Eye-observation, Epifluorescence with camera, Spinning-disc modalities).
	* Point out that we were using the Eye-observation mode all this time		* Point out that we were using the Eye-observation mode all this time
	* Switch to Epifluorescence with camera mode		* Switch to Epifluorescence with camera mode
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	'''Confocal Spinning Disc mode'''		'''Confocal Spinning Disc mode (the main thing you do with this microscope)'''

	* Switch to the Spinning Disc modality		* Switch to the Spinning Disc modality
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	* Point out the lack of out-of-focus blur to highlight the confocality again.		* Point out the lack of out-of-focus blur to highlight the confocality again.
	* Adjust the light intensity and exposure times to show that the same principles apply, you need signals stronger than noise.		* Adjust the light intensity and exposure times to show that the same principles apply, you need signals stronger than noise.
	* Repeat this for another pre-set Optical Configuration.		* Repeat this for another pre-set Optical Configuration.<br />
			'''Camera settings in more detail (worth spending time on this)'''


	'''~~In-depth camera~~ settings (worth spending time on)'''

	* ''Binning'': You can choose to sacrifice resolution to gain sensitivity to low signals by increasing binning		* ''Binning'': You can choose to sacrifice resolution to gain sensitivity to low signals by increasing binning
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	'''[[Nikon sora superresolution switch\|SoRa Superresolution, how to switch on/off (link)]]'''		'''[[Nikon sora superresolution switch\|SoRa Superresolution, how to switch on/off (link)]]'''

	* This should theoretically reach resolutions of ~~ca.~~ 150 nm (~~green~~)		* This should theoretically be able to reach resolutions of around 150 nm (at 510 nm)



			'''ND Acquisition'''

			This is used to do automated multidimensional experiments

			Start with a Z-stack, because the full SoRa pipeline to get maximum resolution needs this.

	~~ND Acquisition for automated multidimensional experiments, start with Z-stack because full SoRa pipeline needs this.~~

Current microscope status

Jelle — Thu, 28 May 2026 14:48:06 GMT

Light microscopes

← Older revision		Revision as of 14:48, 28 May 2026
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	\|-		\|-
	\|[[PhaseView light sheet\|Lightsheet]]		\|[[PhaseView light sheet\|Lightsheet]]
	\|		\|OK
	\|Microscope fully functional, use 4TB SSD drive to take images		\|Microscope fully functional, use 4TB SSD drive to take images
	\|20.11.2025		\|20.11.2025

Nikon sora introduction protocol

Jelle — Thu, 28 May 2026 07:57:50 GMT

Show changes

Nikon sora

Jelle — Tue, 26 May 2026 15:53:46 GMT

correct introduction protocol link

← Older revision		Revision as of 15:53, 26 May 2026
(One intermediate revision by the same user not shown)
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	[[Nikon sora functions\|What can it do?]]		[[Nikon sora functions\|What can it do?]]

	[[Nikon sora ~~switch on~~\|~~How to '''switch on'''~~]]		[[Nikon sora introduction protocol\|Introduction protocol]]

	[[Nikon sora superresolution switch\|How to ~~'''~~switch to superresolution~~'''~~]]		[[Nikon sora switch on\|How to switch on]]

			[[Nikon sora superresolution switch\|How to switch to superresolution]]

	[[Nikon sora lightpath\|Dual camera imaging wavelengths]]		[[Nikon sora lightpath\|Dual camera imaging wavelengths]]

Nikon sora introduction protocol

Jelle — Tue, 26 May 2026 15:52:04 GMT

created page

New page

Introduction protocol

Type of microscope and its strengths
- Spinning disc microscopy for fast confocal microscopy (optical sectioning)
- Suitable for live-cell imaging experiments
- Superresolution optional, to achieve (ideally) ca. 150 nm resolution in green.
- Two-camera option for capturing two fluorescent colors at the same time (dynamic processes)
- Fluorescence Recovery After Photobleaching (FRAP) to study molecular diffusion times

Stage-top incubation system for live-cell imaging (switch on before starting a live cell experiment)
First manual operation and doing Brightfield (finding the sample)
Epifluorescence mode by eye and by camera (quick checking fluorescent signals)
Confocal Spinning Disc mode (in-depth camera settings)
SoRa Superresolution to double resolving power
ND Acquisition for automated multidimensional experiments, start with Z-stack because full SoRa pipeline needs this.
Perfect Focus System for keeping/using exact focus levels in live view and during ND Acquisition experiments

FRAP (optional)
Dual camera mode (optional)

Data saving (nd2 files) and transfering (SURF file sender)
User account creation
Booking system discussion

← Older revision		Revision as of 15:53, 26 May 2026
(One intermediate revision by the same user not shown)
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	[[Nikon sora functions\|What can it do?]]		[[Nikon sora functions\|What can it do?]]

	[[Nikon sora ~~switch on~~\|~~How to '''switch on'''~~]]		[[Nikon sora introduction protocol\|Introduction protocol]]

	[[Nikon sora superresolution switch\|How to ~~'''~~switch to superresolution~~'''~~]]		[[Nikon sora switch on\|How to switch on]]

			[[Nikon sora superresolution switch\|How to switch to superresolution]]

	[[Nikon sora lightpath\|Dual camera imaging wavelengths]]		[[Nikon sora lightpath\|Dual camera imaging wavelengths]]