Leica SP8 Liachroic intro - Revision history

Jelle at 10:02, 23 September 2025

2025-09-23T10:02:50Z

Jelle: additions

2025-08-14T12:20:54Z

additions

← Older revision		Revision as of 12:20, 14 August 2025
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	'''Focusing''' (sample finding, and then moving around, warning: hitting lens to sample possible)		'''Focusing''' (sample finding, and then moving around, warning: hitting lens to sample possible)

	'''Epifluorescence''' (see visually light shining, see returning light, discuss different filters, user responsible for knowing their dyes and wavelengths, Searchlight spectra viewer)		'''Epifluorescence''' (see visually light shining, see returning light, discuss different filters, user responsible for knowing their dyes and wavelengths, Searchlight spectra viewer. This method is used to see where is the signal, is there any signal, do I already see something suitable for confocal imaging?)

	'''Confocal scanning''' (gonna be a big part, mostly on computer now, switch in mood/user to focus on screen not on microscope - instructor sits on the far-right side of the desk to control the mouse, attendees sit right in front of the screen to see everything properly)		'''Confocal scanning''' (gonna be a big part, mostly on computer now, switch in mood/user to focus on screen not on microscope - instructor sits on the far-right side of the desk to control the mouse, attendees sit right in front of the screen to see everything properly)
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	# We start in "Acquire" (top) and will be spending most time there		# We start in "Acquire" (top) and will be spending most time there
	# The big vertical line in the middle divides the view into settings (left) and image display (right)		# The big vertical line in the middle divides the view into settings (left) and image display (right)
	# Making any adjustments to settings in the image display (right) is not going to change any raw data values or any microscope settings - just how the image looks on the screen		# Making any adjustments to settings in the image display (right) is not going to change any raw data values or any microscope settings - just how the image looks on the screen
	# Making adjustments on the left will change actual microscope settings, such as wavelengths used, scanning behavior etc.		# Making adjustments on the left will change actual microscope settings, such as wavelengths used, scanning behavior etc.
	# At the bottom, there are the buttons that make the microscope actually do something (Live, Capture Image, Start - etc.) - to prevent confusion when clicking "open laser shutter" in the software, or any other buttons.		# At the bottom, there are the buttons that make the microscope actually do something (Live, Capture Image, Start - etc.) - to prevent confusion when clicking "open laser shutter" in the software, or any other buttons.
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	# Acknowledge we have a few detectors available, one is switched on.		# Acknowledge we have a few detectors available, one is switched on.
	# Prefer HyD (hybrid detectors), they are better. Typically they are in standard mode with 100 gain (digital gain) and you can use them like that.		# Prefer to always choose HyD (hybrid detectors), they are better. Typically they are in standard mode with 100 gain (digital gain) and you can use them like that. You can destroy the detector by setting its detection window to include the current laser wavelength used (dotted line in detector area spectrum reminds you which lasers are used).
	# PMT detectors are less sensitive = good for strong signals (usually you have weak signals), to use one you have to give it some gain (couple hundred Volts, until image looks good to you)		# PMT detectors are less sensitive = good for strong signals (usually you have weak signals), to use one you have to give it some gain (couple hundred Volts, until image looks good to you)
	# Move the detection window and resize it to capture the desired fluorescence emission wavelengths. Avoid including the laser wavelength at all cost!! This will visualise the laser, which we do not want to see - and it can damage the detector.		# Move the detection window and resize it to capture the desired fluorescence emission wavelengths. Avoid including the laser wavelength at all cost!! This will visualise the laser, which we do not want to see - and it can damage the detector.
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	# Is there nothing there anyway, maybe you need more laser -> Increase laser power to 20-30%, capture another image -> have a look if something shows up.		# Is there nothing there anyway, maybe you need more laser -> Increase laser power to 20-30%, capture another image -> have a look if something shows up.
	# Is there still nothing, maybe the focus is slightly wrong (we're in confocal mode after all...) -> use the Z-adjustment knob to focus up and down (either on the microscope, on the joystick, or on the USB panel) -> have a look if something shows up, now it really should.		# Is there still nothing, maybe the focus is slightly wrong (we're in confocal mode after all...) -> use the Z-adjustment knob to focus up and down (either on the microscope, on the joystick, or on the USB panel) -> have a look if something shows up, now it really should.
	# If there's still nothing, visually check if the sample is still alright, and then use Brightfield or Epifluorescence through the binoculars to find focus again. Then try confocal again, using the software		# If there's still nothing, visually check if the sample is still alright, and then use Brightfield or Epifluorescence through the binoculars to find focus again. Then try confocal again, using the software.
			# If there's still nothing, there is a problem with the microscope or the sample. Change samples to a known working sample - a piece of paper responds to 405 nm, a stroke of Staedler Yellow Highlighter responds to 488 nm.

	- Evaluating the first image		- Evaluating the first image, boundary conditions

	# It could be too weak (barely jumping out of the noise), so we need more laser until it's visible (improving the scan will help too, but this comes later) at the cost of possibly bleaching		# It could be too weak (barely jumping out of the noise), so we need more laser until it's visible (improving the scan will help too, but this comes later) at the cost of possibly bleaching
	# It could be too strong (huge areas look intense, and same intensity - mouse-over the pixel and see the maximum value 255 show up under the picture = too bright!) you want to avoid ~~saturaiton~~		# It could be too strong (huge areas look intense, and same intensity - mouse-over the pixel and see the maximum value 255 show up under the picture = too bright!) you want to avoid saturation.

	- Optimizing the scan (better picture, takes longer, make it as good as you need and not better)		- Optimizing the scan (better picture, takes longer, make it as good as you need - and not better. Every improvement you make can be compared to the previous situation by flipping through the last couple of acquired images)

			# There are three main settings that most influence the image quality, which you can use to maximize the details and signals that the current objective is able to see. (if not enough, you need a higher mag. objective)
			# Format (number of pixels that are scanned -> note that the square area of the sample that you are scanning does not change in size, just gets divided into smaller steps i.e. more measurement points i.e. pixels). This influences the resolution of the image (lower = worse). Use the "Optimize" button on the left of Format to always get the right number of pixels to describe the details that are available through this objective.
			# Speed (lower values = slower, takes longer but results in higher signal-to-noise). This means the laser spends more time on each pixel, and thus illuminates that place for longer, and thus gets more signals if there are signals. Noise always stays the same.

			- Adding a second channel

			# Set up another laser (e.g. 561, if you used 488) to activate the other fluorophores
			# Set up another detector (e.g. HyD3 if you used HyD1) to detect the other fluorophores' signals
			# Do another "Capture Image" and make optimizations where necessary (use the Evaluating the first image section above)

	- Switching to a higher magnification lens (use navigator to register 1 pic, switch to immersion lens, go back to original location).		- Switching to a higher magnification lens (use navigator to register 1 pic, switch to immersion lens, go back to original location).

			# Higher magnification does not automatically mean higher detail on a confocal scanning microscope.
			# Higher NA does mean higher detail on a confocal. Provided that the scan settings are also optimized (just done that, can repeat it).

	- Z-stack (set start, end, use optimized)		- Z-stack (set start, end, use optimized)
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	- Time course (switch modes using dropdown menu, then set (1) interval (none, or amount of time) and (2) duration (unlimited, or amount of time, or amount of pictures)		- Time course (switch modes using dropdown menu, then set (1) interval (none, or amount of time) and (2) duration (unlimited, or amount of time, or amount of pictures)

	- Tilescan (one small one, several of them, focus map)		- Tilescan (one small one, several of them, focus map, stitching)



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	- Leaving room and system tidy for next user		- Leaving room and system tidy for next user


			Optional functions

			- Autofocus

			- Emission wavelength scanning (check whether the signal behaves like the fluorophore should)

			- Closing the pinhole (more resolution, lower signal)

Jelle: drafted most segments and started adding details

2025-08-06T16:35:53Z

drafted most segments and started adding details

@@ Line 1: / Line 1: @@
-'''Intro-Intro'''
+'''Introduction'''
 # Welcome, outline of the introduction
@@ Line 13: / Line 13: @@
 # Log-in in Windows (user will get an account) and software starting
-Stage and objective movement controls (XY stage, Z objectives)
+'''Stage and objective movement controls''' (XY stage, Z objectives, Switch Objectives on the touch screen - start with the 10X lens. You normally start low, then go higher)
-Sample placement (sample types, coverslip towards the bottom, adjusting holder, put demo or user sample there, don't clamp it but let it rest (otherwise breaks when objective hits))
+'''Sample placement''' (sample types, coverslip towards the bottom, adjusting holder, put demo or user sample there, don't clamp it but let it rest (otherwise breaks when objective hits))
-Brightfield mode (where does light come from, what do we expect to see)
+'''Brightfield''' (where does light come from, what do we expect to see)
-Focusing (sample finding, and then moving around, warning: hitting lens to sample possible)
+'''Focusing''' (sample finding, and then moving around, warning: hitting lens to sample possible)
-Epifluorescence mode (see visually light shining, see returning light, discuss different filters, user responsible for knowing their dyes and wavelengths, Searchlight spectra viewer)
+'''Epifluorescence''' (see visually light shining, see returning light, discuss different filters, user responsible for knowing their dyes and wavelengths, Searchlight spectra viewer)
-Confocal scanning mode (gonna be a big part, mostly on computer now, switch in mood/user focus on screen not on microscope)
+'''Confocal scanning''' (gonna be a big part, mostly on computer now, switch in mood/user to focus on screen not on microscope - instructor sits on the far-right side of the desk to control the mouse, attendees sit right in front of the screen to see everything properly)

Jelle at 13:25, 6 August 2025

2025-08-06T13:25:24Z

← Older revision		Revision as of 13:25, 6 August 2025
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	'''~~Introduction~~'''		'''Intro-Intro'''

	# Welcome, outline of the introduction		# Welcome, outline of the introduction
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	# The microscope physically (components, roughly)		# The microscope physically (components, roughly)

	Switch-on		'''Switch-on'''

	# Quick inspection (everything looks ok visually?)		# Quick inspection (everything looks ok visually?)

Jelle: made a start

2025-08-06T13:05:08Z

made a start

← Older revision		Revision as of 13:05, 6 August 2025
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	~~placeholder~~		'''Introduction'''

			# Welcome, outline of the introduction
			# The General Instrumentation department conceptually and physically
			# The room and the general layout
			# The microscope conceptually (functions)
			# The microscope physically (components, roughly)

			Switch-on

			# Quick inspection (everything looks ok visually?)
			# Switch-on procedure of components (buttons numbered order)
			# Log-in in Windows (user will get an account) and software starting

			Stage and objective movement controls (XY stage, Z objectives)

			Sample placement (sample types, coverslip towards the bottom, adjusting holder, put demo or user sample there, don't clamp it but let it rest (otherwise breaks when objective hits))

			Brightfield mode (where does light come from, what do we expect to see)

			Focusing (sample finding, and then moving around, warning: hitting lens to sample possible)

			Epifluorescence mode (see visually light shining, see returning light, discuss different filters, user responsible for knowing their dyes and wavelengths, Searchlight spectra viewer)

			Confocal scanning mode (gonna be a big part, mostly on computer now, switch in mood/user focus on screen not on microscope)

Jelle: created page

2025-08-06T12:45:38Z

created page

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