user guide nil 4 - hyland software

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May 2017

LEXMARK CONFIDENTIAL

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USER GUIDE Nil 4.2

Content:

Page 2 Login Page

Page 3 Patient Study Directory

Page 3 Work Items

Page 9 Search Tools

Page 10 Viewing a Study

Page 10 Post Processing Tools

Page 14 Timeline / Extended Timeline grid

Page 20 Study Tools / Side Bar

Page 29 Modality Specific Functions

Appendices

Page 38 Appendix 1. Annotation Tools

Page 43 Appendix 2. View Modes

Page 54 Appendix 3. Features new to Nil 4.2

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Login Page

User Name

Password

Site: Tenancy – Nil can support Multi-Tenancy i.e. Nil has the ability to federate and use multiple instances

whilst sharing the same infrastructure.

Test your connection speed with Lexmark Server (not client to internet): Tool can be used for

troubleshooting.

Minimum bandwidth: 2 Mbps for clinical/core and 5 Mbps for advanced visualization. Max Latency: 100ms

Note: Bandwidth= size of the ‘pipe’ Latency = Distance it has to travel % = Indication of the quality of the

network

Forgot your password

Connection Type – Optimizes interaction depending on connection type.

Local network –To be used inside the hospital, is faster for study manipulation and scrolling.

Internet – Connection type to be used from outside the hospital. Study manipulation compensates for lower

bandwidths (image titles disappear when scrolling – final image is always full fidelity)

Auto detect should detect the optimal connection when the user logs in.


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Waiting Room:–Live /real time interactive meeting feature Used with Collaboration but when the

recipient does not have an e-mail address. The meeting ID is inserted to gain access. See Collaboration tool.

After logging in, you are taken to the Patient Study Directory:

Patient Study Directory:

Work Items:

Click on the icon next to the Patient Study Directory to minimize the work items.


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Displays patients/studies from all directories across the enterprise on the

Nil Cache /archive

Displays patients from specific directories e.g. PACS or VNA

Lists the studies you have recently opened. Max 50

Displays a list a patients /studies with predefined filters applied e.g. CT,

male, under 16. Can be public or personal

Works like academic folders – patients /studies added to folder for peer

review / MDT meetings etc. Can be public or personal Note: both folders need manual intervention to

remove studies from folder.

Right Click on Worklists / Folders for further functionality:

Load Studies: Loads studies as batch load or a priors. Studies are preloaded so provides a quick workflow

for clinical meetings

Send Study Link: Sends a link via e-mail. The receiving clinician can then view studies in that worklist/folder.

(Clinical application for MDT/Peer review). The recipient is required to have an individual Nil account.

Permissions for this account can be controlled at a system administration level

Copy link: Creates a copy of the link which can be cut and pasted into browser or instant message.

Edit. Characteristics of the worklist/ folder can be edited

Copy: Worklists / folders can be copied to create new one.(Contents not copied)

Delete: Worklists / folders can be deleted


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Top tool bar

Drop box functionality. Service (DICOM Storage SCP) that allows for the secure transfer of

data to and from Nil without a VPN. Imports drop straight onto dropbox which NIL polls regularly and

uploads into NIL. Good for bulk upload workflows.

Uploads DICOM and Non-DICOM (wrapped). Content uploaded from the dropbox must be DICOM

Monitors study transfers from local database to remote DICOM Servers inc. current, completed

and failed transfers.

Nil 4.2 provides a number of methods for uploading studies. Click on ‘Upload New Study and

the following window appears:


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1. Upload DICOM Media:

Upload from CD/DVD/USB or a folder. The media may contain multiple patients / studies. The media MUST

contain a DICOMDIR file.

Either drag and drop folder into drop area or select ‘browse’ to locate the folder.

When uploading, click on the whole folder (Nil will ignore files that should not be uploaded)

Once the folder/media has been selected, click on ‘next’ to show a list of studies to be uploaded.

Click on upload

2. Upload zipped DICOM files.

Upload a .zip file containing DICOM files. The file must only contain DICOM files.

The file may contain multiple patients / studies

Select ‘Browse’ to locate the files and click on ‘upload’

3. Upload folder with DICOM files


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Upload a folder that only contains DICOM files. The folder may contain multiple patients / studies

Drag and drop or navigate via browse to the folder containing the DICOM files.

Click on ‘next’ to display a list of studies to be uploaded.

Select ‘upload’.

4. Upload DICOM Files

Upload individual DICOM files. The files must be from the same location (i.e. same folder) and may contain

multiple patients / studies.

Drag and drop or navigate via browse to the DICOM files.

Click on ‘next’ to display a list of studies to be uploaded.

Select ‘upload’

5. Upload Non-DICOM Files

Upload non DICOM files. Files must be for the same patient and study.

Drag and drop or navigate via browse to the non-DICOM files.

Click on ‘next’ and enter the study details

Select ‘upload’


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6. Create an upload link

Create an encrypted link that other people can use to upload files. The link can be used to upload a .zip file,

individual DICOM and non-DICOM files.

Click on ‘Create Upload Link’ and a new window will appear:

The link can be configured in the following ways:

Allocate a limit to the number of upload session the user is allowed.

Allocate an expiry on the link.

Force the user to login to a Nil account before they can access the upload link OR

Force the user to enter a password before they can access the upload link. The password must

contain at least 8 characters.

Allow the user to upload non-DICOM files.

Once configured, select ‘next’. The upload link appears with an option to copy the link to clipboard for

pasting into e-mail / instant message) or send link via e-mail:


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NB: The available options for uploading are dependent on the browser. (IE does not have ‘Upload folder

with DICOM files’ or ‘upload DICOM media’)

Live /real time interactive meeting feature– ability to set up cross-enterprise meetings. Used

when Collaboration is used but the recipient does not have an e-mail address. The meeting ID is inserted to

gain access.

Refer to appendix 4

Online reference for Nil functionality

Logs off user from active Nil session

Search Tools:

Clears any filters applied to the field headers

Refreshes the search

Customisable column headings. The filters can be set in ‘user configuration’ (4 max)

Resets the customizable column headings.

Columns: these can relocated – drag and drop the headings


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Viewing a Study:

Patient Banner: This displays the patient’s name, DOB, sex with the date and accession number of the

study

Post processing tools:

Note: These are the basic post processing tools; Modality specific tools detailed later.

Vertical mouse scrolling through slices and horizontal scrolling through time (used with multi-

dimensional studies such as cardiac or diffusions scans). Scrolling using the left mouse button initially

displays the images in lossy compressed format so is quick. Once the scrolling stops the full quality image is

displayed. Note: scrolling through the images with the middle mouse tracker ball displays full quality

images.


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Scrolling through Multiframe series also possible by clicking and dragging the scroll tool at

bottom of viewport

Drop down options:

Drag to zoom in and out of image

Drop down options: In MPR mode use rotate to relocate the

position of the axials, sagittals and coronals in the view area.

Inverts black and white

Window width and level adjustments

Box W/L. Window width and level automatically adjusted based on the box region

Used to correct the gamma curve for luminesce when viewing colour images

Edge enhance / blur tool

Zoom window which can be used as an additional overlay view port, there are an additional

subset of tools within the view port.

Now available in 2D and 3D Reference lines are shown on all series on the current screen that are in

the same frame of reference. The intersection of the reference lines represents the corresponding position

in all viewports. Works in conjunction with reference lines (use relate to move the reference lines)


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Links 2 series together. It allows you to scroll through the linked series in a synchronized manner.

Changes (such as rotation and zoom) applied to one series are also applied to the other series

Sub- menu of all annotation tools available to a user. See appendix 1 for further details

Marks significant images as ‘key’ and adds them as a new key image series. Only available with 2d

images

Removes the DICOM overlay information from the image

Views the original uncompressed image. (Used in mammography to guarantee the image is

lossless and all pixel data is displayed)

Resets all changes applied to image

Use close down current viewport. Use Open to reopen.

Hanging Protocols (Clinical and Interpretation licenses only). Protocols to define

how images/ studies are displayed. HP’s can be assigned and created from here. Refer to appendix 5 for full

instructions.


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Defines how the studies are laid out on the screen e.g. 1x2 split with current study on left and

most recent prior on right. Drop down options:

Pre-defined view ports. E.g. US images from same series displayed in 4x4 format on screen. The

View function contains all modality / specialty specific viewing tools. Refer to appendix 2.

Show or hide reference lines. Note: Use Relate to change the position of the reference lines.

Displays study as a movie. Expands when selected:

Cine scroll options:

Pressing the space bar on the keyboard will stop the cine run.

Saves the current display. 3 Options:

Saves the display as a new presentation (presentation state) and can be edited

Captures a screen grab as a new series. Cannot be edited. When more than 1 screen grabs are

captured in the same session they will appear in the same series.


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Exports the display as a jpeg

Takes the user back to the patient directory

Simply closes the study down. Does not close Nil

Logs the user off the current instance of Nil

Post processing tools are also available when the user right clicks on the image. See Appendix 3 for all right

click functions.

Timeline:

Load a study from the timeline by either clicking on it or by dragging into a viewport.


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If the icon on the time line is a square as opposed to a circle then it is on the XDS registry.


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Extended Timeline Grid

The extended timeline can be used to preview studies and filter the display of specific studies in the

timeline.

Select the filter icon at the right of the timeline.

NB: The figure below the icon indicates the number of studies available and the number currently filtered to

be displayed.

A new window appears:

There are 2 panes. The top pane details the available studies. The lower pane provides additional preview

information.

The studies are listed in the upper pane with the following column headers:

Study number (Chronological, as appears on timeline)

Source (data source)

Newer (Identifies studies newer than the anchored study)


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Performed on

Modality

Accession Number

Number of images

Study description.

Filtering the studies to be displayed in the timeline:

1. Select the studies using the following options:

All: Displays all priors

Manual Selection: Allows the user to manually select from the grid which studies to display.

Filtered: Allows filtering by Age, Modality and Description

Enter age, modality and description (keywords) into the available fields to filter the grid. Select newer to

display newer studies than the anchor study.

These filters can be configured through hanging protocols.

2. Select ‘set as relevant’


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The selected studies will appear on the timeline along with the anchor study.

Previewing the studies:

Preview the highlighted study in the grid by selecting one of the following options:

Study info: Patient demographics and DICOM information for the study is displayed in the lower pane.

Reports: Available reports are displayed in the lower pane

Images: Thumbnails for each series appear in the lower pane.

Images from each series can be viewed by clicking on the corresponding thumbnail. A new window


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appears with the images displayed. Note: the only tools available within this viewport are the mouse

functions and a scroll tool.

To launch the selected study within the full Nil application click on ‘load’ (bottom left of screen)

Hovering over the study displays the properties:

The timeline can be minimized / maximized from the viewport. Display and content of the timeline can be

controlled using hanging protocols (application preferences) or in user preferences.


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Study Tools / Sidebar

The study tools can be found at the left of the screen and can be minimized using the green arrow. Display of

the tools can be controlled using hanging protocols (application preferences) or by configuring user

preferences

Collaboration Tool:

The Collaboration tool enables online/ real-time, interactive meetings between clinicians where single or

batch loaded patients +/or studies can be reviewed. The participants do not need to have a Nil Account.

When selected the following options appear:

Nil supports Skype integration (configured in user accounts and user preferences).


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Collaboration: Click on ‘share’ to open a control panel for the meeting pop up options. This is a movable

window and can be moved away from image data.

The Meeting ID will be shown at the top left of this window:

Users can either notify the participating clinicians of the meeting ID (where it can be used to gain access

through the ‘Waiting Room’) or clicking the ‘invite’ tool, will launch the desktop email application, so that a

link to the waiting room can be sent via email:


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Enter meeting ID and username and click “Join”

This will open a new instance of Nil for the invitee to collaborate with original user. The original user will see

that an invitee has attended:

Users will now be able to watch the original user and any movements they make on screen.


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If appropriate, select an attendee and pass over control to allow the invited user to control the screen.

Then Collaboration session will automatically end if the original user quits the collaboration session or exists

Nil.


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User will be notified and the session closed/ locked. For security, they will be unable to continue with the

meeting if the original user is not logged in.

NB. Multiple patients can be viewed during the collaboration session if loaded as ‘batch load’ from the

patient directory.


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Presets.

These are post processing tools that can be applied to visualize different aspects of a study. The presets are

configured and loaded according the modality, study view and rendering mode.

E.g. A 2d CT study will have the following presets assigned:

A 3d CT has these presets assigned:


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Presentations

Presentations are used to save annotations and measurements and can be pushed back to the VNA /PACS

using a lifecycle rule. (Only available in Interpretation)

To create a presentation, apply annotations / measurement to image. Go to the side panel and open

presentations.

Right click on the ‘draft’ and select ‘approve’

An approved presentation cannot be modified and is shown with dashed lines. A label in the bottom left

corner will contain the word ‘Approved’ with the approval date.

If you approve or delete a draft presentation during the session, a new draft is NOT automatically created.

To create a new one, right click on the existing approved presentation and select ‘make draft’.

If you do not create a new draft and try to apply annotations /measurements, you are given the choice to

either:

‘Make a new draft presentation which you can use to save your changes’ or,


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‘Allow transient in-session overlays’. This will allow you apply annotations and measurements

during your current session but they will not be saved. In this case the word ‘transient’ will appear

at the bottom left corner of the viewport.

Note: Presentations originating from 3rd party applications such as a VNA or PACS will also appear here.

They will already have an approved status and appear with the following icon:

View Tools:

Modality specific visualization tools. (Advanced tools in Interpretation license only). For advanced 3D the

following ‘clipper’ tools are available:

The clipper tools are used to selectively remove anatomy from 3d rendered images. Segment Tools: Used to

view and edit tissues.


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Series: The available series appear here. The user can also configure the settings so that a ‘virtual single

stack’ of images from all series is created

(Settings, preferences, modality preferences – select the modality and choose ‘create combined series’)

An ‘eye’ icon will appear on the series being currently viewed.

The series description and number of images will appear in each thumbnail.

Other Icons:

Multi- image series

Cine series

Multi-frame series


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Multi-dimensional series e.g. Cardiac (when scrolling through a multi-dimensional study the

horizontal scroll moves through time and the vertical scroll moves through position.)

Modality specific functionality.

Nuclear Medicine / PET CT (Interpretation license only)

Assigns a colour map to nuclear medicine images. Drop down:

Assigns a colour map to fusion images. Drop down:


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Adjusts the fusion blend level.

Mammography (Interpretation License Only)

Quadrant Zoom. Provides a magnified view of 4 quadrants. Zooms the image by a factor of

1:8. Select quadrant zoom from toolbar. Choose the quadrant to zoom by either clicking with the tool:

Or use the dropdown menu to select:


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CAD (Computer Aided Detection) is supported (Interpretation license only). Studies with CAD will appear in

the view tools:

Hovering over the CAD icon displays the CAD report summary.

The full CAD report appears as a SR in the timeline:

Click on ‘show CAD’ to display on image

CAD information is also displayed on Digital Breast Tomosynthesis (DBT) Studies.

Mammography studies have special fast prior scrolling functions- ‘next prior’ and ‘previous prior’ are

commands that can be mapped to the mouse/keyboard


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Ophthalmology. (Interpretation License Only)

Filters study to display either right or left eye only

Displays right eye only (opto-dextra)

Displays left eye only (opto-sinistro)

Alters the blend level of red-green laser images

Smart Zoom function provides additional view port functionality:

To assist visualization of the eyes, if the screen is split 1x2 and ‘link’ is selected, the ‘pan’ tool moves the

images in opposite directions.


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Pathology (Interpretation License Only). See Pathology teaching guide for further information.

Microscopy slides can be zoomed using the virtual microscopy tool embedded in the image:

A colour balance tool is available for pathology:


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Radiotherapy (Interpretation and Clinical License Only)

Nil can be used to view Radiotherapy treatment plans.

Note: Nil should not be used for approving plans.

The plans include the following features:

Isodoses (Displays areas receiving equal doses of radiation)

Structures (Displays anatomical structures)

Beams (Displays external radiation beams)

RT Graph (Dose volume histogram)

DRR (Digitally reconstructed radiograph)

Select the RT tools from the study tools:

Select the required plan by click on the drop down menu under ‘plan’

Select Isodoses, structures or the beams from the category menu


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Isodoses: Isodoses can be selected /deselected:

Structures can be selected /deselected:


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Beams can be selected / deselected

To display the RT graph, select from RT graph from the View tools menu

First select the structures from the category menu.

The dose for each structure is displayed:

Hover over each label for information on dose.


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To display the DRR (digitally reconstructed radiograph) select DRR from the view tools menu

Select the beam and the control point.

The treatment field position for the beam are displayed.

The rectangle represents the jaw pairs

The inner area represents the multi-leaf collimators.


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Appendix 1. Annotations tools.

Basic Annotations (available in Interpretation license)

Click on the image to initiate the arrow and drag the mouse towards the feature or focal point,

unclicking to finish the arrow. A text box will appear for arrow labels/ notes

Use to add text to an image

The text can be relocated by clicking on dotted line and dragging to new position.

Click and drag vertically to create vertical line. Click and drag horizontally to create horizontal. The

lines can be moved.


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Drag to draw and curve between 2 points. The curve can be moved or adjusted.

Click and drag to create free-form annotations

Identification of vertebrae. Once selected, click on a vertebrae e.g. L1 and the following pop up

appears:

Select the correct corresponding vertebrae, then click on each vertebrae in turn (moving in sequence) and

the spine is labelled:

Click on ‘Study’ to extend the labelling to all the images in the current study. ‘Not shared’ limits the

labelling to the open viewport only.


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Click to display a point intensity measurement e.g. Hounsfield Units

Click and drag to create a linear measurements. (Measurements are shown with a ** when the pixel

calibration data is missing from the dicom tags. ‘Measurements estimated’ appears on the overlay.)

Click and drag to create a free hand measurement

Create a multi-segmented line and measurement. Click on multiple points in a line.

Create a ratio between 2 lines. E.g. CTR

Used when image is not calibrated (e.g. analogue, scanned image). ‘User calibrated’ appears on the

overlay.

Used to create a circular ROI Statistics for the area are shown as appropriate for the study type -:

Average / Max intensity, Average / Max SUV, standard deviation, area and main diameters.


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Use to create a freehand border around a region of interest using. Statistics for the area are shown

as appropriate for the study type (for example: average intensity, standard deviation, area and main

diameters).

Use to create an elliptical border around a region.

Used with Ophthalmology images. Used to work out ratio of 2 different circular areas.

Drag to create the first side of the angle (the start of this side will be the vertex). Click where you

want to place the bottom of the second side of the angle. The two sides are automatically connected. The

angle between the two sides is shown.

Used to measure spinal deformities such as scoliosis. Drag to create the first side of the Cobb

angle, then drag to create the second side. The two sides are automatically connected. The angle between

the two sides is shown.

The colour of the annotations can be changed.

Delete the last or all annotations from the current image. Use ‘reset’ to

delete annotations from the whole study. The user can also delete and annotation by right clicking on it and

selecting delete.


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Basic Annotations available in Clinical license:


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Appendix 2: View Modes

View function contains all modality / specialty specific viewing tools.

View Modes available in Interpretation license:

Splits the view port of 2d images into various layouts.

Splits images into Multi-planar reformat views:


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Displays axials, coronals and sagittal images in slab format. The thickness of the slices can be altered

using the thickness icon on the post processing tool bar:

Displays axials, coronals and sagittal images in a 2x2 format

Displays axial images

Displays coronal images

Displays sagittal images

The user can create a curved MPR. Use edit and add in view tools to place a series on markers on a

piece of curved anatomy (vessel) to create the MPR.


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Name and save the newly created MPR by clicking on the save icon in the post processing tool bar.

Vessel Tracer (Interpretation License Only)

Enables the user to identify and review vessels on CT with contrast studies.

Open CT series and select Vessel tracer from View Tools

A new window appears with 7 viewports.

1: Contains 3D image

2, 3 and 4: Axial, Coronal and Sagittal MPR views

5: Stretched ribbon view of the vessel. This can be edited

6: Curved reformat of vessel identifying the location on the cross-sectional view

7: Cross section view of vessel –details minimum and maximum diameter and area of lumen.

To create the vessel views:


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Click on View Tools.

Click on ‘New’ to add a series of points along the vessel to be traced. (You can add points whilst scrolling

through the series)

The completed views appear in viewports 5, 6 and 7

Delete will remove the points

Undo will remove the last point added

Name the trace and click on save. Saved traces can be accessed by selecting the ‘vessel’ number from the

dropdown menu.

The ribbon view can be edited using the 3 edit functions: points, centre line and wall

To position the cross section view, either use the middle mouse key to drag the cross hair line into the

required position or select ‘points’ and click on the required position.

Selecting MPR on vessel will localize the 3 MPR views on the vessel.

Auto window level optimizes the W/L of the vessel


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Displays fusion views on NM and CT

NM (white) and CT (dark grey) in 2x2 layout with fused axial (shaded grey) in lower left viewport

NM (white) and CT (dark grey) in a 3x3 layout with fused axials (shaded grey) in lower row

NM (white) and fused images (shaded grey) in 2x2 layout.

NM (white) and fused images (shaded grey) in 2x3 layout

Fused Slab images in unsymmetrical layout

NM (white) and fused (shaded grey) in unsymmetrical layout

Fused slab images in 1x3 layout

Radiotherapy Graph and Digitally Reconstructed Radiograph. (see Modality

specific functions)


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Note: The ECG module is only available in clinical and interpretation. Core will only display the captured

ECG image.

Displays the trace in a rhythm layout

Displays the trace in a matrix layout

Individual leads can be selected/deselected:

Note The ECG display has a standard ECG paper grid where a small 1mmx1mm box represents 40 ms time

and 0.1 mV amplitude and a large 5mmx5mm box with 200 ms and 0.5 mV. The small/large boxes may be

hidden depending on the zoom factor.

You can edit a video to remove unwanted sections. The newly created video is added as a new series. The

original video remains as an unmodified series.

Open a video series and click on ‘video editor’.

The following tools appear:


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The top control bar contains all the tools required to edit the video.

The bottom timeline contains thumbnail images of the video content.

To edit a video select sections of the video you wish to keep.

Follow these steps to edit your video:

1. Select the sections you wish to keep by dragging the frame indicator to the start position, and select

the ‘set segment start’ tool:


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2. Drag the frame indicator to the end position and select the ‘set segment end’ tool.

You see the selected segment of video outlined in green:

3. If required, reposition the start and end points by dragging the start or end points into position.

NB: When the video editor is first opened, the entire video defaults as ‘selected’ and is outlined in green.

4. To add additional segments, click on ‘add segment’ and a new box will appear:

5. To remove a segment click on the ‘remove segment’ tool:


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6. Review the edited video. Select one of the options in the drop down menu adjacent to ‘Play result’ to

select either to play the resulting edit, selected segment or the original. Click on the ‘play’ icon to

review the video.

7. The speed of the playback can be altered using the slider to change the speed.

8. Loop the playback by selecting the ‘loop’ icon.

9. Move to the start or end of the segment/video by selecting the following

10. Move frame by frame through the video by selecting the following

11. Click on the ‘pause’ icon to pause the playback.

12. Save the new editing video clip by clicking on the ‘save’ icon

13. Choose the encoding profile from the dropdown menu. The profile determines the quality and file

size.

14. If there is sound with the video, select audio on or off.

15. The new video will be saved as a new series


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Timeline tools:

Scroll through the thumbnails using the arrows at each side of the thumbnail bar.

Increase the number of thumbnails on the timeline (the size will reduce)

Use to fit all thumbnails on the timeline

Use to reduce the number of thumbnails on the timeline (the size will increase)

Alter the volume of the video sound


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May 2017


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View Modes available in Clinical license:

View Modes in Core license:


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May 2017


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Doc #990-07003

Appendix 3. New Features in Nil 4.2

1. ‘Recently opened’ worklist

2. Extended Timeline Grid

3. Video Editor

4. Additional series information added to thumbnails

5. Cine playback enhancements

6. Advanced Confidentiality masks

7. Upload enhancements

8. Download encapsulated studies in original format (e.g. MP4)

9. Close / open icon

10. Ability to download from Acuo

11. Data QC Module (see Data QC teaching guide)


user guide nil 4 - hyland software

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