Nikon sora introduction protocol - Revision history

Jelle at 15:40, 28 May 2026

2026-05-28T15:40:07Z

← 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.~~

Jelle at 07:57, 28 May 2026

2026-05-28T07:57:50Z

← Older revision		Revision as of 07:57, 28 May 2026
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	[[Nikon sora switch on\|'''Switch-on procedure''']]		[[Nikon sora switch on\|'''Switch-on procedure''']] (link)

	* Make sure to also start the software already and start Single-cam mode		* Make sure to also start the software already and start Single-cam mode
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	SoRa Superresolution to ~~double resolving power~~		'''[[Nikon sora superresolution switch\|SoRa Superresolution, how to switch on/off (link)]]'''

			* This should theoretically reach resolutions of ca. 150 nm (green)

Jelle at 07:56, 28 May 2026

2026-05-28T07:56:25Z

← Older revision		Revision as of 07:56, 28 May 2026
Line 20:		Line 20:

	* 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
			* Component 3 needs to be switched on and is already on the right settings.
	* Look at the stage-top incubator itself - it has a lid that should be used during the experiment		* Look at the stage-top incubator itself - it has a lid that should be used during the experiment
	* There is a plastic removable frame covering a "canal" (basin) of water around the edge of the sample area		* There is a plastic removable frame covering a "canal" (basin) of water around the edge of the sample area

Jelle at 16:34, 27 May 2026

2026-05-27T16:34:40Z

← Older revision		Revision as of 16:34, 27 May 2026
Line 9:		Line 9:
	* 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]]~~


	[[Nikon sora switch on\|'''Switch-on procedure''']]		[[Nikon sora switch on\|'''Switch-on procedure''']]
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	* 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
	~~First manual operation~~


	'''First manual operations'''		'''First manual operations'''
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	* 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.
	~~First brightfield operation~~


	'''First brightfield observation'''		'''First brightfield observation'''
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	* 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.



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

Jelle at 16:34, 27 May 2026

2026-05-27T16:34:14Z

← Older revision		Revision as of 16:34, 27 May 2026
Line 1:		Line 1:
	'''Introduction protocol'''		=== '''Introduction protocol''' ===

	Type of microscope and its strengths
			'''Type of microscope and its strengths'''

	* Spinning disc microscope for fast confocal microscopy (optical sectioning)		* Spinning disc microscope for fast confocal microscopy (optical sectioning)
Line 8:		Line 9:
	* 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]]

	[[Nikon sora switch on\|Switch-on procedure]]		[[Nikon sora switch on\|'''Switch-on procedure''']]

	* Make sure to also start the software already and start Single-cam mode		* Make sure to also start the software already and start Single-cam mode
	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 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
Line 20:		Line 24:
	* 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
			First manual operation

	First manual ~~operation~~		'''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.
Line 28:		Line 33:
	* 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.
			First brightfield operation

	First brightfield ~~operation~~		'''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
Line 44:		Line 50:


	Epifluorescence mode by camera (quick checking fluorescent signals)		'''Epifluorescence mode by camera (quick checking fluorescent signals)'''

	* Go to the computer and make sure everyone can see the screen		* Go to the computer and make sure everyone can see the screen
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	Confocal Spinning Disc mode (in-depth camera settings)		'''Confocal Spinning Disc mode'''

			* Switch to the Spinning Disc modality
			* Activate a pre-set, e.g. "488"
			* Point out that it now looks different but we will also go step-by-step
			* Point out that there are now 5 lasers available
			* Capture Image and inspect the result
			* Live view and adjust laser and exposure time to get decent signal
			* Point out that we are now in confocal mode and the optical section is thinner than before
			* Let the user move the focus up/down and see clearly different layers of the sample, especially noticable because it's in confocal mode
			* 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.
			* Repeat this for another pre-set Optical Configuration.

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

			* ''Binning'': You can choose to sacrifice resolution to gain sensitivity to low signals by increasing binning
			* ''Bit-depth'': Always 16-bit, because it has the most accurate intensity registration. 12-bit doesn't make sense to use for any obvious reason.
			* ''Exposure time'': Adjust in multiples of 5. You can show what happens with an exposure time of 2 ms (stripes!)
			* ''Scan mode'': Always on "Fast" (the other ones are just doing on-chip averaging to get more signal-to-noise, whereas you can just increase exposure time to achieve the same).
			* ''Full-sensor or smaller sensor area (custom)'': Start with full-sensor always. The only application for a smaller sensor size is when you need extremely rapid imaging, as those images will then be smaller in data-size to transfer from the camera to the computer.

Jelle at 16:27, 27 May 2026

2026-05-27T16:27:10Z

← Older revision		Revision as of 16:27, 27 May 2026
Line 1:		Line 1:
	'''Introduction protocol'''		'''Introduction protocol'''


	Type of microscope and its strengths		Type of microscope and its strengths
Line 9:		Line 8:
	* 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]]		[[Nikon sora switch on\|Switch-on procedure]]

	* Make sure to also start the software already and start Single-cam mode		* Make sure to also start the software already and start Single-cam mode

	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 on before starting a live cell experiment)

Line 31:		Line 28:
	* 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.


	First brightfield operation		First brightfield operation

Jelle at 16:26, 27 May 2026

2026-05-27T16:26:45Z

@@ Line 1: / Line 1: @@
-Introduction protocol
+'''Introduction protocol'''
@@ Line 11: / Line 11: @@
 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)
+* Go to the computer and make sure everyone can see the screen
 Confocal Spinning Disc mode (in-depth camera settings)
@@ Line 44: / Line 91: @@
-Booking system discussion
+Booking system

Jelle at 16:08, 27 May 2026

2026-05-27T16:08:00Z

← Older revision		Revision as of 16:08, 27 May 2026
Line 4:		Line 4:
	Type of microscope and its strengths		Type of microscope and its strengths

	* Spinning disc ~~microscopy~~ for fast confocal microscopy (optical sectioning)		* Spinning disc microscope for fast confocal microscopy (optical sectioning)
	* Suitable for live-cell imaging experiments		* Suitable for live-cell imaging experiments
	* Superresolution optional, to achieve (ideally) ca. 150 nm resolution in green.		* 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)		* 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



	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 on before starting a live cell experiment)

Jelle at 16:07, 27 May 2026

2026-05-27T16:07:41Z

← Older revision		Revision as of 16:07, 27 May 2026
Line 1:		Line 1:
	Introduction protocol		Introduction protocol

	* Type of microscope and its strengths
			Type of microscope and its strengths

	* Spinning disc microscopy for fast confocal microscopy (optical sectioning)		* Spinning disc microscopy for fast confocal microscopy (optical sectioning)
	* Suitable for live-cell imaging experiments		* Suitable for live-cell imaging experiments

Jelle at 15:55, 26 May 2026

2026-05-26T15:55:17Z

← Older revision		Revision as of 15:55, 26 May 2026
Line 1:		Line 1:
	Introduction protocol		Introduction protocol

	Type of microscope and its strengths		* 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

	~~- 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)		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)		First manual operation and doing Brightfield (finding the sample)


	Epifluorescence mode by eye and by camera (quick checking fluorescent signals)		Epifluorescence mode by eye and by camera (quick checking fluorescent signals)
	Confocal Spinning Disc mode (in-depth camera settings)		Confocal Spinning Disc mode (in-depth camera settings)


	SoRa Superresolution to double resolving power		SoRa Superresolution to double resolving power


	ND Acquisition for automated multidimensional experiments, start with Z-stack because full SoRa pipeline needs this.		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		Perfect Focus System for keeping/using exact focus levels in live view and during ND Acquisition experiments


	FRAP (optional)		FRAP (optional)


	Dual camera mode (optional)		Dual camera mode (optional)


	Data saving (nd2 files) and transfering (SURF file sender)		Data saving (nd2 files) and transfering (SURF file sender)


	User account creation		User account creation


	Booking system discussion		Booking system discussion