Documentation
2D+Time Measurement Data
Documentation
3D Measurement Data
Table of contents
Image View: Web Deep Zoom Toolkit
The Web Deep Zoom Toolkit (WDZT) is designed to visualize big images across multiple frames and layers.
Toolbar
The toolbar contains the following buttons:-
Show or hide all menus of interactive control modules.
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Zoom in.
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Zoom out.
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Go back to the original image view where the entire image
is visible.
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Switch to full screen mode.
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Exit full screen mode.
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Go to the first frame.
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Go to previous frame.
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Enter the movie mode. In the movie mode, each next frame is displayed
after 2.5 seconds.
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Pause the movie mode.
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Go to next frame.
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Go to the last frame.
Interactive Control Modules
Modules are automatically added or removed depending on the type of an information layer being displayed.Layer selection
The layer selection module allows one to change the displayed information layer.The frame number, zoom and position are preserved when changing layers of similar types.
Layer composition
The layer composition is designed to display multiple layers on top of each others.The layer selected in this Layer composition module is displayed on top of the one selected in the Layer selection module.
The opacity of the added top layer is adjustable with the slider ranging from transparent (left - not visible) to opaque (right - fully visible).
If multiple layers are added, one can set the stack order by dragging and dropping the arrows or text of the composition labels.
Display info
- Cursor information
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Display information about the current cursor position. The information is
updated every time the cursor stops hovering over the image panel.
- Image coords
- Position of a cursor in the coordinate system of the entire image.
- Screen coords
- Position of a cursor in the coordinate system defined by the image displayed currently.
- Intensity
- Intensity of the pixel defined by the cursor position.
- Acquired intensity
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Approximative intensity of the pixel under the
cursor as it was acquired before conversion to
8bpp.
Not available on all datasets.
- Field of view info
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Display information about the current field of view. The information is
updated every time the field of view changes.
- Zoom
- Current zoom. 100% means original image resolution, 50% means half the original image resolution, etc... This percentage is similar to the one used by image processing programs such as ImageJ.
- X, Y, width and height
- Position of the current field of view in the entire image. X and Y represent the upper left corner of the field of view.
Colony searching
Enter a colony number and press Enter to highlight its bounding box in the image.
Screen recording
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Take a snapshot of the current screen and download it as a zip
file along with the provenance informations (see below).
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Activate the recording mode. This mode is designed for recording
an image every time a frame or an information layer has changed. This could be
achieved by pressing the play button of the toolbar and
interactively browsing the image while recording frames.
The recording operation is performed in RAM on the client side, and the recorded images with the provenance file are compressed into a zip file. A user can download the zip file by clicking on the folder icon (
)
that appears after the stop recording button
(
)
is clicked. During the recording, the system
checks the cumulative file size and pops up a warning dialog
when the size exceeds a few MB.
Both snapshot and recording modes gather information about the image layer, its frame index and zoom level, and the viewed window in pixels for each recorded image. This information is stored in a provenance file together with the name of the recorded image file.
The Options section supports publications of images with interesting content. It allows a user to include a scale bar and a timestamp in the downloaded images as watermarks.
The recording mode might consume a lot of RAM memory over a longer period of recording time. This could lead to a browser crash if too many frames are recorded. If this is the case then please consider using the data fetching module.
Data fetching
This module is designed to sample images by specifying the field
of view and the zoom. By default, the currently displayed field
of view is fetched. One can customize the field of view by checking
"Manually set bounds". This enables a user to enter the desired
zoom and field of view into the editable fields under the
"Fetching bounds" panel.
The "layers to fetch" panel allows to select which layers to
download. Multiple layers can be selected and they will be
downloaded in separate zip files .
The "Frame range" field is for specifying which frames to sample.
For example, entering 1-5,14-16,20 into the "Frame range" edit
box will lead to downloading frames 1, 2, 3, 4, 5, 14, 16 and
20.
The sampling and downloading are triggered by clicking the
"Fetch" button. It performs image sampling computations
on the server side using java code. The computations include
image extraction, compression of images into a zip file, and creation of
the corresponding provenance information inserted into the zip file.
The download will start automatically when the sampling
computations are finished on the server.
When using the data fetching module, the images are provided in their original format (if available), usually 16 or 32 bits per pixel (bpp) and in uncompressed tif image file format.
Scalebar options
- Display scale bar
- Uncheck to hide the scale bar.
- Location
- Select from four corner locations for the placement of a scale bar.
- Color
- Select black or white color of the scale bar.
- Background
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If checked then add a semi-transparent background.
If the scale bar is white then the background will be black.
If the scale bar is black then the background will be white.
Display transitions
The display transitions module is activated for x-y-energy datasets from material science, side view.
This module allows to enter the energy transition lines to be overlaid on the image display.In the text input, one should enter a chemical element symbol to select the element's transitions to be overlaid on the image display.
The elements symbols follow the periodic table conventions.
The color coding for energy lines follows the colors of the molecular visualizer Jmol.
Nearby transitions
The display transitions module is activated for x-y-energy datasets from material science, side view.
The nearby transitions module display the proximity ranked list of all transitions close to the cursor position."Energy" corresponds to the energy level under the cursor.
The nearby transitions in the table are sorted by proximity to the cursor (the closest appears first).
The table is updated every time the cursor move over the image.
Colony features
The colony features module is activated for x-y-time datasets from cell biology.
A left click on a colony will trigger a display of its
bounding box and centroid, and a pop-up dialog with all
pre-computed colony features. The information about each colony
is presented in a distinct color so that multiple colonies can be
explored simultaneously.
For details on the colony features, refer to the
Stem Cell Features help.
Distance measurement
This module allows to measure and display distance after selecting a starting point and an ending point on an image display. To enable this function, the first step is to activate the module by clicking the checkbox "Active Measurement". After choosing the starting point and the ending point, the module will show the measurements on the left side of the image.
This module also provides the functions of removing measurement and exporting the measurements to CSV file.
Reminder: Remember to uncheck the "Active Measurement" checkbox when completing the interaction using this wizard in order to enable full functionality of other interaction wizards.
Object Fetching
The frame identification ("FID") field is for specifying which frames. For example, entering 1-5 14-16 20 <5 >150 into the "FID" edit box will lead to downloading frames 1, 2, 3, 4, 5, 14, 16,20 and any frame ID greated than 150. Another example shown in Figure 14 illustrates 3 selected colony objects, 3 ranges of frames, and also 2 layers.
The downloading are triggered by clicking the "Fetch" button. The download will start automatically after the zip file is prepared on the server.
The zip file contains images and provenance information file.
Reminder: Please remember to uncheck the "Active Object Fetching" checkbox when completing the interaction using this wizard in order to enable full functionality of other interaction wizards.