Image5D

Image5D

Author: Joachim Walter (walter at biz.uni-muenchen.de)

Source: Contained in Image_5D.jar, which can be opened using a ZIP utility

Installation: Image5D, which is now maintained by the ImageJDev project (imagejdev.org) is available at imagejdev.org/plugins/image5d.

Description: These plugins extend image stacks to 5 dimensions: x, y, channel (color), slice (z), frame (t). Unlike the HyperVolume Browser, an Image5D has a "true" 5D format. That way plugins working on stacks should usually work as expected on the currently displayed stack of an Image5D (just try a z-projection to see what this means). Image5Ds are displayed in a window with two scrollbars for slice and time below the image and a panel with controls to change the current channel and its color to the right of the image. A dropdown menu allows to change the display of the channels. Options are one channel in gray, one channel in color and an overlay of selected channels.

In the one channel color and overlay modes one can open a panel to select the display color of a channel or to edit a more refined LUT with the ImageJ LUT Editor.
To create an Image5D, use the plugins "Open Series as Image5D", "Stack to Image5D" or "RGB to Image5D".
Open Series as Image5D opens a series of images or stacks from harddisk and converts it to an Image5D. Stack to Image5D converts an already opened stack to an Image5D, and RGB to Image5D converts an RGB image or stack to an Image5D.
Missing features:

Saving just saves the current stack, not the full dataset.
Calibration functions do not work.
Converting the type (8-bit, 16-bit, float) does not work.
Display changes in overlay mode are SLOW.
Known bugs: none so far
A sample 5D data set is available. In consists of HeLa cells with an H2B-GFP construct to stain the chromatin imaged in fluorescence and transmission. A large part of the GFP fluorescence is bleached in the second frame and the cells go through mitosis, later. It has 2 channels, 24 slices and 7 frames. The file (mitosis-5d.zip) is a TIFF stack contained in a ZIP archive. To view it with Image5D, open it using File/Open or drag and drop, then convert it to an Image5D using Plugins/Image5D/Stack to Image5D.
A sample 16-bit RGB data set of triple labeled cloned myoblast cells is also available. To view it with Image5D, open it using File/Open or drag and drop, then convert it to an Image5D using Plugins/Image5D/Stack to Image5D. This image is courtasy of Dr. Angelica Keller and Juliette Peltzer, Faculte des Sciences et Technologies, Universite Paris 12 Val de Marne, France.

See Also: Sync Windows and Sync Measure 3D
Spectral Unmixing Plugins
TransformJ, FeatureJ, RandomJ and MTrackJ

History: 2005/06/03
First version

2005/06/17 (version 1.1)
Included the HyperVolume Opener plugin into Image5D. The HyperVolume Opener is called from the Open_Stack_As_Image5D plugin.
The HyperVolume Opener uses Windows XP style file sorting, i.e. digits appearing in the filename are treated as numbers and sorted accordingly. This works nicely with filenames of the style name-<ch>-<z>-<t>.tif even if the numbers <ch>... don't have leading zeros.
Overwrote getImageStack() to return an ImageStack (not an Object[]). In the end this will make it possible to save Image5Ds.
Added the method "public String getI5DMetaData()" to return Image5D specific metadata for saving. Currently an empty string is returned.
Checking ImageJ version in Stack_to_Image5D and RGB_to_Image5D plugins.

2005/06/23 (version 1.1.1)
Fixed a bug in "Open Series as Image5D" that could lead to a wrong datastack size when a directory contains several Hypervolumes.

2005/06/25 (version 1.1.2)
Fixed a bug in the setStack() method that led to incorrect cooperation with the TransformJ plugins.

2005/10/24 (version 1.1.4)
Speeded up display by a factor of at least two by caching.
Added support of calibration functions.
Added Saving and Loading of Image5Ds, including metadata. Metadata includes (beyond the usual metadata for ImageJ stacks) lookup tables and contrast and brightness values.
Added a Plugin to transfer the colormaps and channel labels of one open Image5D to another one ("Transfer_Channel_Settings").
Added a Plugin to make z-Projections of Image5Ds ("Z_Project")
Added a Plugin to make montages of Image5Ds ("Make_Montage")
Inherited ImagePlus.flush(). This fixed a memory leak.
Added a Plugin to convert the current timeframe of an Image5D to an RGB stack using the current view settings ("Image5D_Stack_to_RGB").
Added a Plugin to Convert an Image5D to an ImageStack ("Image5D_to_Stack").
Modified the "RGB_to_Image5D" plugin so that Hypervolumes containing z- and t- information can be converted.
Added a Plugin to create a new Image5D ("New_Image5D").
Added a Plugin to select the displayed channel/slice/timeframe and the display mode ("Set_Position").
Added a Plugin to change the display state (display in overlay / as gray) of a channel ("Set_Channel_Display").
Added a Plugin to change the labels of the channels of an Image5D ("Set_Channel_Labels").
The last three plugins give Image5D some macro scripting capability.

2005/10/24 (version 1.1.5)
The HyperVolumeOpener copies the calibration across from the first image in a series (Feature by Jonathan Jackson)
Fixed a bug in Open_Image5D, so that the pixel width, height, depth and frame interval are now read correctly. (Bug reported by Erik Meijering)
Added a button, which enables selecing the color of a channel by a Dialog with three sliders for RGB. The three-slider RGB-Dialog is also opened by double-clicking on the Color Palette of the color selector.
Added the plugin "Virtual_Image5D_Opener" to open file series as Image5Ds from disk. I.e. just the currently displayed data is in RAM. Everything else is on disk.
Added an option to the Transfer_Channel_Settings plugin to copy the DensityCalibrations from one Image5D to another Image5D.
Corrected a bug that would cause an exception with the montage and z-project plugins when single frames were processed with output as Image5D selected.
Recommendation: Erik Meijering updated his TransformJ, FeatureJ, RandomJ and MTrackJ plugins to work with Image5Ds.

2006/10/05 (version 1.1.7)
The z-/t-/ch-changer (slider, or selector for the channel in overlay mode) is only displayd when the size of the respective dimension is >1.
Image5Ds react smoother to resizing.
The Image5D_stack_to_RGB plugin transfers the calibration of the Image5D to the resulting RGB stack. This feature was proposed by Jerome Mutterer.
The Hypervolume_Opener now ignores .roi-files and calculates the increments starting from the "start"-value (i.e. as one would expect). This change was proposed by Jonathan Jackson.
Added keyboard shortcuts for selecting the current channel, slice and frame:
   channel: PageDown and PageUp or numpad 7 and 8
   slice: shift-PageDown and PageUp or numpad 4 and 5
   frame: ctrl-PageDown and PageUp or numpad 1 and 2
   This feature was proposed by Michael Murray.

Added a rudimentary "about" dialog that can be used to check the installed Image5D version.

2006/09/20 (version 1.1.6)
Restructured to use Java packages. The previous version (Image_5D_1.1.5.jar) is available for use with the PerkinElmer plugin as of September 2006.

2007/08/14 (version 1.2.0)
Added a "Tiled" display mode, that displays all color channels on separate canvases in the same window. ROIs are shown in all channels. Copy/paste and most tools from the ImageJ toolbar work in the channel canvases.
Added a plugin to duplicate an Image5D.
Scrollbars for selecting ch/z/t are no longer blinking on Windows.
Enabled using the getInfo("image.subtitle") macro function for Image5Ds. Fix provided by Sebastien Huart (Sebastien.Huart_AT_curie.fr)
Added Mousewheel control of Channels and Frames (like the slice slider of the Stack Window). Pressing shift while moving the wheel moves the frame ("shi-F-t as in Frame"). Pressing ctrl while moving the wheel moves the channel ("C-trl as in Channel").
Adapted modifiers (Ctrl/Shift) of keyboard shortcuts to match the Mousewheel modifiers: channel: ctrl-PageDown and PageUp or numpad 7 and 8 slice: PageDown and PageUp or numpad 4 and 5 (no modifier) frame: shift-PageDown and PageUp or numpad 1 and 2 - The "Transfer Channel Settings" and the "Set Channel Display" plugins are now macro-recordable.
The values of all channels at the current cursor location are displayed in the statusbar in overlay and tiled mode. - Image5Ds now display the slice labels in the info line.
In the "Stack to Image5D" plugin, the default choice of dimension orders (ch/z/t) now conforms to the order in ImageJ.
Fixed a bug that caused the Image5D returned by the "Stack to Image5D" plugin was not the current image.

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Author:	Joachim Walter (walter at biz.uni-muenchen.de)
Source:	Contained in Image_5D.jar, which can be opened using a ZIP utility
Installation:	Image5D, which is now maintained by the ImageJDev project (imagejdev.org) is available at imagejdev.org/plugins/image5d.
Description:	These plugins extend image stacks to 5 dimensions: x, y, channel (color), slice (z), frame (t). Unlike the HyperVolume Browser, an Image5D has a "true" 5D format. That way plugins working on stacks should usually work as expected on the currently displayed stack of an Image5D (just try a z-projection to see what this means). Image5Ds are displayed in a window with two scrollbars for slice and time below the image and a panel with controls to change the current channel and its color to the right of the image. A dropdown menu allows to change the display of the channels. Options are one channel in gray, one channel in color and an overlay of selected channels. In the one channel color and overlay modes one can open a panel to select the display color of a channel or to edit a more refined LUT with the ImageJ LUT Editor. To create an Image5D, use the plugins "Open Series as Image5D", "Stack to Image5D" or "RGB to Image5D". Open Series as Image5D opens a series of images or stacks from harddisk and converts it to an Image5D. Stack to Image5D converts an already opened stack to an Image5D, and RGB to Image5D converts an RGB image or stack to an Image5D. Missing features: Saving just saves the current stack, not the full dataset. Calibration functions do not work. Converting the type (8-bit, 16-bit, float) does not work. Display changes in overlay mode are SLOW. Known bugs: none so far A sample 5D data set is available. In consists of HeLa cells with an H2B-GFP construct to stain the chromatin imaged in fluorescence and transmission. A large part of the GFP fluorescence is bleached in the second frame and the cells go through mitosis, later. It has 2 channels, 24 slices and 7 frames. The file (mitosis-5d.zip) is a TIFF stack contained in a ZIP archive. To view it with Image5D, open it using File/Open or drag and drop, then convert it to an Image5D using Plugins/Image5D/Stack to Image5D. A sample 16-bit RGB data set of triple labeled cloned myoblast cells is also available. To view it with Image5D, open it using File/Open or drag and drop, then convert it to an Image5D using Plugins/Image5D/Stack to Image5D. This image is courtasy of Dr. Angelica Keller and Juliette Peltzer, Faculte des Sciences et Technologies, Universite Paris 12 Val de Marne, France.
See Also:	Sync Windows and Sync Measure 3D Spectral Unmixing Plugins TransformJ, FeatureJ, RandomJ and MTrackJ
History:	2005/06/03 First version 2005/06/17 (version 1.1) Included the HyperVolume Opener plugin into Image5D. The HyperVolume Opener is called from the Open_Stack_As_Image5D plugin. The HyperVolume Opener uses Windows XP style file sorting, i.e. digits appearing in the filename are treated as numbers and sorted accordingly. This works nicely with filenames of the style name-<ch>-<z>-<t>.tif even if the numbers <ch>... don't have leading zeros. Overwrote getImageStack() to return an ImageStack (not an Object[]). In the end this will make it possible to save Image5Ds. Added the method "public String getI5DMetaData()" to return Image5D specific metadata for saving. Currently an empty string is returned. Checking ImageJ version in Stack_to_Image5D and RGB_to_Image5D plugins. 2005/06/23 (version 1.1.1) Fixed a bug in "Open Series as Image5D" that could lead to a wrong datastack size when a directory contains several Hypervolumes. 2005/06/25 (version 1.1.2) Fixed a bug in the setStack() method that led to incorrect cooperation with the TransformJ plugins. 2005/10/24 (version 1.1.4) Speeded up display by a factor of at least two by caching. Added support of calibration functions. Added Saving and Loading of Image5Ds, including metadata. Metadata includes (beyond the usual metadata for ImageJ stacks) lookup tables and contrast and brightness values. Added a Plugin to transfer the colormaps and channel labels of one open Image5D to another one ("Transfer_Channel_Settings"). Added a Plugin to make z-Projections of Image5Ds ("Z_Project") Added a Plugin to make montages of Image5Ds ("Make_Montage") Inherited ImagePlus.flush(). This fixed a memory leak. Added a Plugin to convert the current timeframe of an Image5D to an RGB stack using the current view settings ("Image5D_Stack_to_RGB"). Added a Plugin to Convert an Image5D to an ImageStack ("Image5D_to_Stack"). Modified the "RGB_to_Image5D" plugin so that Hypervolumes containing z- and t- information can be converted. Added a Plugin to create a new Image5D ("New_Image5D"). Added a Plugin to select the displayed channel/slice/timeframe and the display mode ("Set_Position"). Added a Plugin to change the display state (display in overlay / as gray) of a channel ("Set_Channel_Display"). Added a Plugin to change the labels of the channels of an Image5D ("Set_Channel_Labels"). The last three plugins give Image5D some macro scripting capability. 2005/10/24 (version 1.1.5) The HyperVolumeOpener copies the calibration across from the first image in a series (Feature by Jonathan Jackson) Fixed a bug in Open_Image5D, so that the pixel width, height, depth and frame interval are now read correctly. (Bug reported by Erik Meijering) Added a button, which enables selecing the color of a channel by a Dialog with three sliders for RGB. The three-slider RGB-Dialog is also opened by double-clicking on the Color Palette of the color selector. Added the plugin "Virtual_Image5D_Opener" to open file series as Image5Ds from disk. I.e. just the currently displayed data is in RAM. Everything else is on disk. Added an option to the Transfer_Channel_Settings plugin to copy the DensityCalibrations from one Image5D to another Image5D. Corrected a bug that would cause an exception with the montage and z-project plugins when single frames were processed with output as Image5D selected. Recommendation: Erik Meijering updated his TransformJ, FeatureJ, RandomJ and MTrackJ plugins to work with Image5Ds. 2006/10/05 (version 1.1.7) The z-/t-/ch-changer (slider, or selector for the channel in overlay mode) is only displayd when the size of the respective dimension is >1. Image5Ds react smoother to resizing. The Image5D_stack_to_RGB plugin transfers the calibration of the Image5D to the resulting RGB stack. This feature was proposed by Jerome Mutterer. The Hypervolume_Opener now ignores .roi-files and calculates the increments starting from the "start"-value (i.e. as one would expect). This change was proposed by Jonathan Jackson. Added keyboard shortcuts for selecting the current channel, slice and frame: channel: PageDown and PageUp or numpad 7 and 8 slice: shift-PageDown and PageUp or numpad 4 and 5 frame: ctrl-PageDown and PageUp or numpad 1 and 2 This feature was proposed by Michael Murray. Added a rudimentary "about" dialog that can be used to check the installed Image5D version. 2006/09/20 (version 1.1.6) Restructured to use Java packages. The previous version (Image_5D_1.1.5.jar) is available for use with the PerkinElmer plugin as of September 2006. 2007/08/14 (version 1.2.0) Added a "Tiled" display mode, that displays all color channels on separate canvases in the same window. ROIs are shown in all channels. Copy/paste and most tools from the ImageJ toolbar work in the channel canvases. Added a plugin to duplicate an Image5D. Scrollbars for selecting ch/z/t are no longer blinking on Windows. Enabled using the getInfo("image.subtitle") macro function for Image5Ds. Fix provided by Sebastien Huart (Sebastien.Huart_AT_curie.fr) Added Mousewheel control of Channels and Frames (like the slice slider of the Stack Window). Pressing shift while moving the wheel moves the frame ("shi-F-t as in Frame"). Pressing ctrl while moving the wheel moves the channel ("C-trl as in Channel"). Adapted modifiers (Ctrl/Shift) of keyboard shortcuts to match the Mousewheel modifiers: channel: ctrl-PageDown and PageUp or numpad 7 and 8 slice: PageDown and PageUp or numpad 4 and 5 (no modifier) frame: shift-PageDown and PageUp or numpad 1 and 2 - The "Transfer Channel Settings" and the "Set Channel Display" plugins are now macro-recordable. The values of all channels at the current cursor location are displayed in the statusbar in overlay and tiled mode. - Image5Ds now display the slice labels in the info line. In the "Stack to Image5D" plugin, the default choice of dimension orders (ch/z/t) now conforms to the order in ImageJ. Fixed a bug that caused the Image5D returned by the "Stack to Image5D" plugin was not the current image.