1.Download the .jar file using the link below:
| Version | Link |
|---|---|
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Download |
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In ImageJ/Fiji installation directory, paste the .jar file in the plugins directory
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Restart Fiji
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The plugin can be found in ImageJ/Fiji Plugin menu
1 : The process mode selection
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SINGLE_FILE: perform projection of the image selected in file path field (9) and save the output to the same directory of the input
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MULTIPLE_FILES: batch processing and saving of all the .tif images in directory path field (10)
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PREVIEW: show the output image in a new window with a sub dialog for calibrating the parameters; multiple preview windows can be opened simultaneously
2 : Reference channel selection
For image with multiple channels, a channel must be selected as the reference channel. The surface projection is performed on only the reference channel and the output Z-map is applied on other channel.
The default selection is the first channel
3 : The Direction of the Stack
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OUT : The image stack is captured starting from inside the object and ending at the surface
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IN : The image stack is captured starting from surface and moving inside the object
4 : Envelope Stiffness
The distance[pixels] between the peaks in the Z-map of the surface projection; the higher the stiffness, the less noise and smoother the surface projection become. This should be tuned starting from stiffness=1 and increase until the output is the desire projection
5 : Filter Size
The filter size for the median filter step. The median filter step helps in smoothing the z-map and contribute to the final smoothness. This can be set starting at around 10 and increase if needed
6 : Offset
Move the Z-map of the surface projection into the stack
If the Direction (3) is OUT; set Offset to negative number since the surface at the high Z value, it needs to be subtracted to move into the stack
If the Direction (3) is IN; set Offset to positive number since the surface at the low Z value, it needs to be added to move into the stack
This should be kept at 0 if not needed
7 : Depth
Add more intensity to the final projection by including more layers; This should be kept at 0 if not needed
8 : path to the directory for MULTIPLE_FILES Mode
9 : path to the image for SINGLE_FILE and PREVIEW mode
10 : select the desired output files (Maximum intensity Projection(MIP) file, Z Map of the MIP, the Surface Projection, z map of the surface projection )
11 : status bar to show the notification to th users
12 : Progress bar to show the progress of the current projection
13 : Button to start the Surface Projection after all the parameters above have been selected
14 : Cancel button to close the plugin