FIJI - Microscope Measurement Tools - Revision history

John d: switch image example

2019-06-10T18:02:29Z

switch image example

← Older revision		Revision as of 18:02, 10 June 2019
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	Calibrations for NanoFab microscopes are pre-loaded in this UCSB-specific fork of the plugin.		Calibrations for NanoFab microscopes are pre-loaded in this UCSB-specific fork of the plugin.

	(You will need to record the microscope name & objective used when you initially save your photos in the lab.)~~[[File:MicroscopeMeasurementTools - FIJI draw measurement - line.png\|alt=Example of measurements draw on a microscope image\|none\|thumb\|534x534px\|Example of measurements drawn on a microscope image]]~~		(You will need to record the microscope name & objective used when you initially save your photos in the lab.)
	[[File:FIJI MMT UCSB-Fork Choose Microscope Calibration drop down.png\|alt=Screenshot of Drop-Down list of calibrations for UCSB microscopes.\|none\|thumb\|450x450px\|Drop-Down list of calibrations for UCSB microscopes.]]		[[File:FIJI MMT UCSB-Fork Choose Microscope Calibration drop down.png\|alt=Screenshot of Drop-Down list of calibrations for UCSB microscopes.\|none\|thumb\|450x450px\|Drop-Down list of calibrations for UCSB microscopes.]]
			[[File:MicroscopeMeasurementTools - FIJI draw measurement - line.png\|alt=Example of measurements draw on a microscope image\|none\|thumb\|450x450px\|Example of measurements drawn on a microscope image]]

	== Software ==		== Software ==

John d: imge of calibrations list

2019-06-10T18:00:46Z

imge of calibrations list

← Older revision		Revision as of 18:00, 10 June 2019
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	This plugin for FIJI allows UCSB NanoFab users to make calibrated measurements on microscope and SEM images with freely available software, after the image acquisition.		This plugin for FIJI allows UCSB NanoFab users to make calibrated measurements on microscope and SEM images with freely available software, after the image acquisition.

			Calibrations for NanoFab microscopes are pre-loaded in this UCSB-specific fork of the plugin.

		⚫	(You will need to record the microscope name & objective used when you initially save your photos in the lab.)[[File:MicroscopeMeasurementTools - FIJI draw measurement - line.png\|alt=Example of measurements draw on a microscope image\|none\|thumb\|534x534px\|Example of measurements drawn on a microscope image]]
			[[File:FIJI MMT UCSB-Fork Choose Microscope Calibration drop down.png\|alt=Screenshot of Drop-Down list of calibrations for UCSB microscopes.\|none\|thumb\|450x450px\|Drop-Down list of calibrations for UCSB microscopes.]]

	== Software ==		== Software ==
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	** This can not be undone without reloading the image, so be sure to use '''''Save As…'''''.		** This can not be undone without reloading the image, so be sure to use '''''Save As…'''''.
	** You can make a new Overlay before applying the Drawing to make the line moveable or erasable.		** You can make a new Overlay before applying the Drawing to make the line moveable or erasable.
			**
⚫	**[[File:MicroscopeMeasurementTools - FIJI draw measurement - line.png\|alt=Example of measurements draw on a microscope image\|none\|thumb\|~~450x450px~~\|Example of measurements ~~draw~~ on a microscope image]]

	== SEM Images ==		== SEM Images ==

John d: /* Installation */ image size

2019-06-10T17:48:28Z

Installation: image size

← Older revision		Revision as of 17:48, 10 June 2019
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	::* On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:		::* On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:
	::: [[File:MicroscopeMeasurementTools_-_FIJI_Install_-_Mac_Show_Package_Contents.png\|border\|~~150x150px~~]]		::: [[File:MicroscopeMeasurementTools_-_FIJI_Install_-_Mac_Show_Package_Contents.png\|border\|209x209px]]
	:::		:::
	:::		:::

John d: image broder

2019-06-10T17:47:57Z

image broder

← Older revision		Revision as of 17:47, 10 June 2019
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	::* On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:		::* On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:
			::: [[File:MicroscopeMeasurementTools_-_FIJI_Install_-_Mac_Show_Package_Contents.png\|border\|150x150px]]
	::: [[File:MicroscopeMeasurementTools - FIJI Install - Mac Show Package Contents.png\|217x217px]]
			:::
	:::		:::
	::: [[File:FIJI Install Directory - MacOS.png\|alt=Screenshot: MacOS - Where to place the Analyze folder.\|none\|thumb\|630x630px\|MacOS - Where to place the Analyze folder.]]		::: [[File:FIJI Install Directory - MacOS.png\|alt=Screenshot: MacOS - Where to place the Analyze folder.\|none\|thumb\|630x630px\|MacOS - Where to place the Analyze folder.]]

John d: /* Installation */ spacing

2019-06-10T17:46:09Z

Installation: spacing

← Older revision		Revision as of 17:46, 10 June 2019
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	::* On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:		::* On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:
	::: [[File:MicroscopeMeasurementTools - FIJI Install - Mac Show Package Contents.png\|217x217px]]		::: [[File:MicroscopeMeasurementTools - FIJI Install - Mac Show Package Contents.png\|217x217px]]
			:::
	::: [[File:FIJI Install Directory - MacOS.png\|alt=Screenshot: MacOS - Where to place the Analyze folder.\|none\|thumb\|630x630px\|MacOS - Where to place the Analyze folder.]]		::: [[File:FIJI Install Directory - MacOS.png\|alt=Screenshot: MacOS - Where to place the Analyze folder.\|none\|thumb\|630x630px\|MacOS - Where to place the Analyze folder.]]
	# Copy the '''''Analyze''''' folder from MMT into the FIJI '''''Scripts''''' folder.		# Copy the '''''Analyze''''' folder from MMT into the FIJI '''''Scripts''''' folder.

John d: /* Installation */ tabs images

2019-06-10T17:45:40Z

Installation: tabs images

John d: inserted images, corrections

2019-06-10T17:40:32Z

inserted images, corrections

← Older revision		Revision as of 17:40, 10 June 2019
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	== Installation ==		== Installation ==
	# Download ~~FIJI and~~ the Microscope Measurement Tools ~~packages~~.		# Download the [https://github.com/demisjohn/Microscope-Measurement-Tools-UCSB/archive/master.zip Microscope Measurement Tools package]. (Will be referred to as MMT for the rest of the tutorial.)
			# [http://fiji.sc Download FIJI]
	# Install FIJI accordingly.		# Install FIJI accordingly.
	# Unzip the Microscope Measurement Tools ~~(aka. MMT)~~ file~~. Locate the `Analyze` folder inside the package~~.		# Unzip the Microscope Measurement Tools file.
	# ~~Navigate to~~ the ~~FIJI `Scripts`~~ folder, in		## Locate the '''''Analyze''''' folder inside the package.
			# Navigate to the FIJI '''''Scripts''''' folder, in '''''FIJI.app / plugins / Scripts'''''
	## FIJI.app/etc. {{todo\|get path}}
			## On Windows, the folder looks like this:
⚫	# Copy the `Analyze` folder from MMT into the FIJI `Scripts` folder.
			##[[File:MicroscopeMeasurementTools - FIJI Install Directory - WinXP.jpg\|alt=Screenshot: Windows - Where to place the Analyze folder.\|none\|thumb\|474x474px\|Windows - Where to place the Analyze folder.]]
⚫	## In the off chance that an `Analyze` folder already exists in the FIJI scripts folder, merge the two rather than overwriting. You must have placed another script in the same menu location.
			## On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:
			## [[File:MicroscopeMeasurementTools - FIJI Install - Mac Show Package Contents.png\|217x217px]]
			##[[File:FIJI Install Directory - MacOS.png\|alt=Screenshot: MacOS - Where to place the Analyze folder.\|none\|thumb\|630x630px\|MacOS - Where to place the Analyze folder.]]
		⚫	# Copy the '''''Analyze''''' folder from MMT into the FIJI '''''Scripts''''' folder.
		⚫	## In the off chance that an '''''Analyze''''' folder already exists in the FIJI scripts folder, merge the two rather than overwriting. You must have placed another script in the same menu location.
	# (Re)Launch FIJI.		# (Re)Launch FIJI.
	## There should now be a new menu option in `Analyze > Microscope Measurement Tools`		## There should now be a new menu option in '''''Analyze > Microscope Measurement Tools'''''

	=== Add shortcut keys ===		=== Add shortcut keys ===
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	* Download an image from one of our microscopes on Nanofiles.		* Download an image from one of our microscopes on Nanofiles.
	** You must know which microscope and '''which objective the image was saved with'''.		** You must know which microscope and '''which objective the image was saved with'''.
	* Open the image in FIJI		* Open the image in FIJI (or open a copy to avoid overwriting the file)
	* Run the script `Analyze > Microscope Measurement Tools > Choose Microscope Calibration...`		* Run the script '''''Analyze > Microscope Measurement Tools > Choose Microscope Calibration...'''''
	* Select the appropriate microscope and objective from the list and click ~~{{todo\|Apply}}~~		* Select the appropriate microscope and objective from the list and click '''''OK'''''
	** The calibration has now been applied to the image. Any FIJI functions will now use the correct scaling.		** The calibration has now been applied to the image. Any FIJI functions will now use the correct scaling.
	* Enable the Line tool. Draw anywhere on the image you want to measure.		* Enable the Line tool. Draw anywhere on the image you want to measure.
	** While dragging, the FIJI control window will show the calibrated measurement value of your line.		** While dragging, the '''''(FIJI is just ImageJ)''''' control window will show the calibrated measurement value of your line.
	* To draw the measurement on the image, select the menu `Analyze > Microscope Measurement Tools > Draw Measurement - Line`		* To draw the measurement on the image, select the menu '''''Analyze > Microscope Measurement Tools > Draw Measurement - Line'''''
	** This can not be undone without reloading the image, so be sure ~~not~~ to Save ~~the file~~.		** This can not be undone without reloading the image, so be sure to use '''''Save As…'''''.
	** You can make a new Overlay before applying the Drawing to make the line moveable or erasable.		** You can make a new Overlay before applying the Drawing to make the line moveable or erasable.
			**[[File:MicroscopeMeasurementTools - FIJI draw measurement - line.png\|alt=Example of measurements draw on a microscope image\|none\|thumb\|408x408px\|Example of measurements draw on a microscope image]]

	== SEM Images ==		== SEM Images ==
	Images saved from the JEOL SEM automatically save a Text file with the same name, which contains the scaling information.		Images saved from the [[Field Emission SEM 2 (JEOL 7600F)\|JEOL SEM]] automatically save a Text file with the same name, which contains the scaling information.

	As long as this text file is kept in the same location as the image file, the function `Choose Microscope Calibration >> JEOL SEM - AutoCal from TXT` will set the measurement scale appropriately.		As long as this text file is kept in the same location as the image file, the function '''''Choose Microscope Calibration >> JEOL SEM - AutoCal from TXT''''' will set the measurement scale appropriately.

	== References ==		== References ==
	* The original general-use plugin can be found here: Microscope Measurement Tools on GitHub.		* The original general-use plugin can be found here: [https://github.com/demisjohn/Microscope-Measurement-Tools Microscope Measurement Tools on GitHub.]
	* ~~Other~~ FIJI plug-ins available.		* Many other FIJI plug-ins [https://imagej.net/Category:Plugins are available here].
	* Setting the scale on any image with FIJI or ImageJ.		* [https://imagej.net/Spatial_Calibration Setting the scale on any image with FIJI or ImageJ].

John d: Initial instruction, no links

2019-06-07T06:26:03Z

Initial instruction, no links

New page

This plugin for FIJI allows UCSB NanoFab users to make calibrated measurements on microscope and SEM images with freely available software, after the image acquisition.

== Software ==
* FIJI is an open source package, based on ImageJ, for scientific image analysis across many disciplines.
** Download here.

* Microscope Measurement Tools (UCSB Fork) is a plug-in with pre-configured settings that provides the scaling factors for the UCSB NanoFab microscopes and SEMs. It also contains a script for drawing line measurements onto an image.
** This just automates the use of the `Set Scale...` built-in function.

== Installation ==
# Download FIJI and the Microscope Measurement Tools packages.
# Install FIJI accordingly.
# Unzip the Microscope Measurement Tools (aka. MMT) file. Locate the `Analyze` folder inside the package.
# Navigate to the FIJI `Scripts` folder, in
## FIJI.app/etc. {{todo|get path}}
# Copy the `Analyze` folder from MMT into the FIJI `Scripts` folder.
## In the off chance that an `Analyze` folder already exists in the FIJI scripts folder, merge the two rather than overwriting. You must have placed another script in the same menu location.
# (Re)Launch FIJI.
## There should now be a new menu option in `Analyze > Microscope Measurement Tools`

=== Add shortcut keys ===
Optionally add a shortcut key to execute the scripts.

{{todo|add steps}}

== Make a Measurement on an Image ==
* Download an image from one of our microscopes on Nanofiles.
** You must know which microscope and '''which objective the image was saved with'''.
* Open the image in FIJI
* Run the script `Analyze > Microscope Measurement Tools > Choose Microscope Calibration...`
* Select the appropriate microscope and objective from the list and click {{todo|Apply}}
** The calibration has now been applied to the image. Any FIJI functions will now use the correct scaling.
* Enable the Line tool. Draw anywhere on the image you want to measure.
** While dragging, the FIJI control window will show the calibrated measurement value of your line.
* To draw the measurement on the image, select the menu `Analyze > Microscope Measurement Tools > Draw Measurement - Line`
** This can not be undone without reloading the image, so be sure not to Save the file.
** You can make a new Overlay before applying the Drawing to make the line moveable or erasable.

== SEM Images ==
Images saved from the JEOL SEM automatically save a Text file with the same name, which contains the scaling information.

As long as this text file is kept in the same location as the image file, the function `Choose Microscope Calibration >> JEOL SEM - AutoCal from TXT` will set the measurement scale appropriately.

== References ==
* The original general-use plugin can be found here: Microscope Measurement Tools on GitHub.
* Other FIJI plug-ins available.
* Setting the scale on any image with FIJI or ImageJ.

← Older revision		Revision as of 17:45, 10 June 2019
Line 9:		Line 9:

	== Installation ==		== Installation ==
	# Download the [https://github.com/demisjohn/Microscope-Measurement-Tools-UCSB/archive/master.zip Microscope Measurement Tools package]. (Will be referred to as MMT for the rest of the tutorial.)		# Download the [https://github.com/demisjohn/Microscope-Measurement-Tools-UCSB/archive/master.zip Microscope Measurement Tools package]. (Will be referred to as "''MMT''" for the rest of the tutorial.)
	# [http://fiji.sc Download FIJI]		# [http://fiji.sc Download FIJI]
	# Install FIJI accordingly.		# Install FIJI accordingly.
	# Unzip the ~~Microscope~~ ~~Measurement~~ ~~Tools file~~.		# Unzip the downloaded MMT zipfile.
	## Locate the '''''Analyze''''' folder inside the package.		## Locate the '''''Analyze''''' folder inside the package.
	# Navigate to the FIJI '''''Scripts''''' folder, in '''''FIJI.app / plugins / Scripts'''''		# Navigate to the FIJI '''''Scripts''''' folder, in '''''FIJI.app / plugins / Scripts'''''
	## On Windows, the folder looks like this:		::* On Windows, the folder looks like this:
	##[[File:MicroscopeMeasurementTools - FIJI Install Directory - WinXP.jpg\|alt=Screenshot: Windows - Where to place the Analyze folder.\|none\|thumb\|474x474px\|Windows - Where to place the Analyze folder.]]		::: [[File:MicroscopeMeasurementTools - FIJI Install Directory - WinXP.jpg\|alt=Screenshot: Windows - Where to place the Analyze folder.\|none\|thumb\|474x474px\|Windows - Where to place the Analyze folder.]]

	## On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:		::* On Mac, first Right-click FIJI.app and choose "'''''Show Package Contents'''''", and the folder will look like this:
	## [[File:MicroscopeMeasurementTools - FIJI Install - Mac Show Package Contents.png\|217x217px]]		::: [[File:MicroscopeMeasurementTools - FIJI Install - Mac Show Package Contents.png\|217x217px]]
	##[[File:FIJI Install Directory - MacOS.png\|alt=Screenshot: MacOS - Where to place the Analyze folder.\|none\|thumb\|630x630px\|MacOS - Where to place the Analyze folder.]]		::: [[File:FIJI Install Directory - MacOS.png\|alt=Screenshot: MacOS - Where to place the Analyze folder.\|none\|thumb\|630x630px\|MacOS - Where to place the Analyze folder.]]
	# Copy the '''''Analyze''''' folder from MMT into the FIJI '''''Scripts''''' folder.		# Copy the '''''Analyze''''' folder from MMT into the FIJI '''''Scripts''''' folder.
	## In the off chance that an '''''Analyze''''' folder already exists in the FIJI scripts folder, merge the two rather than overwriting. You must have placed another script in the same menu location.		## In the off chance that an '''''Analyze''''' folder already exists in the FIJI scripts folder, merge the two rather than overwriting. You must have placed another script in the same menu location.
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	** This can not be undone without reloading the image, so be sure to use '''''Save As…'''''.		** This can not be undone without reloading the image, so be sure to use '''''Save As…'''''.
	** You can make a new Overlay before applying the Drawing to make the line moveable or erasable.		** You can make a new Overlay before applying the Drawing to make the line moveable or erasable.
	**[[File:MicroscopeMeasurementTools - FIJI draw measurement - line.png\|alt=Example of measurements draw on a microscope image\|none\|thumb\|~~408x408px~~\|Example of measurements draw on a microscope image]]		**[[File:MicroscopeMeasurementTools - FIJI draw measurement - line.png\|alt=Example of measurements draw on a microscope image\|none\|thumb\|450x450px\|Example of measurements draw on a microscope image]]

	== SEM Images ==		== SEM Images ==