I’m glad to present you my toolset focused on visualization and handling of stacks and hyperstacks :
Visualization_toolset.ijm (29.6 KB)
Future uptades will be released on GitHub.
It is based on my own basic needs in the lab, prior to any analysis :
With all new confocal images, give them nice color LUTs, adjust the contrasts, visualize all channels
and save them all as they are in a specific directory.
I hope that some will find this tool useful and I look forward to your feedback!
This toolset provides tools for single images :
Set image LUTs : (up to 5)
A dialog let you select LUTs for each channels and then apply them to your multichannel image.
Auto-contrast Adjustment :
- Especially usefull for stacks (but not restricted to), this macro resets the min and max based on the entire stack so you can navigate through slices without signal saturation.
For multichannel visualization, Splitview creates a RGB montage of composite and splited channels.
Grayscale splitview creates a linear montage with colored overlay and grey channels.
You can still navigate through slices or frames.
Tools for all opended images :
Set all LUTs :
applies the chosen LUTs to all opened images.
Reset all contrasts :
Adjust the contrast to all channels of all opened images.
Maximum Z project all :
Will run a maximal intensity projection on all opended stacks, close the stacks and run “Tile” to see all windows.
Can be handy to get a quick overview of hyperstacks content.
Save all :
Saves all opened images as Tiff in a specified directory.
The must-have macro shortcut : (from Nick George)
- [Q] easy switch between Color and Composite mode on multichannel images
A collection of keyboard shortcuts for tools and additionnal shortcuts for what I think are frequently used commands when handling stacks or hyperstacks:
Macro shortcut :
- [A] Enhance Contrast, saturated=0.3 : almost same as “Auto” button in Brightness tool
- [r] Auto-contrast on active channel of selected image
- [R] Auto-contrast on all channels of selected image
- [S] Colored splitview tool
- [p] Grayscale splitview
Numerical keys shortcuts for basic LUTs:
- [n1] Grays
- [n2] Green
- [n3] Red
- [n4] Cyan
- [n5] Magenta
- [n6] yellow
Frequently used commands :
- [E] Tile : reorder windows to see all
- [y] Open the usefull tool ‘synchronize windows’
- [q] Arrange channels order
- [d] Split Channels
- [M] Merge channels
- [D] Duplicate (complete image or selection)
- [g] Z projection dialog
- [G] run a maximal intensity projection
- [T] Save as Tiff
- Place the Visualization_toolset.ijm file in the toolset directory of your ImageJ or Fiji application.
- Find the toolset in the toolset menu of imageJ bar ( [>>] button).
Finally, I wrote the Visualization_Toolset.ijm file in the most readable way possible (I did my best) in order to be easily customized or adjusted. For example if you don’t like keyboard shortcuts, you can delete them or change the [key].