3Dicom F&E-Funktionsliste

3Dicom F&E-Funktionsliste

Anton
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The 3Dicom R&D software is intended as a fully-featured DICOM viewer and STL viewer software that operates across Windows, MacOS / OS X, and standalone Virtual Reality systems.

Intended for use not as a medical device, but as a powerful tool for medical device manufacturers for R&D, for veterinary usage in small animal surgical planning and particularly for training and education of anatomy and pathology, 3Dicom R&D has a huge number of features which even include medical AI training and validation toolkits.

Discover the full feature set below.

Medical Image & CAD File Management

User can access a ‘Scan Database’ which has tabs at the top for “Local”, “MFTP”, “PACS” and “3D Models”
Load DICOM files into the software from a local directory by clicking “Scan Database”, then clicking on the ‘Local’ tab and then “Load DICOM” button to browse to a local folder containing .DCM extensions
Load NiFTi (.NII) files into the software from a local directory by clicking “Scan Database”, then clicking on the ‘Local’ tab and the “Load Other” button and browsing to a folder containing .NII extensions
Load a compressed folder containing DICOM or NiFTi files into the software from a local directory by clicking “Scan Database”, then on the ‘Local’ tab and “Load Other” button and browsing to a .tar.gz file type (no ZIP and no RAR files)
Search/Filter the Scan Database by Patient Name, Study ID or Series ID in any of the ‘Local’, ‘MFTP’, ‘PACS’ or ‘3D Model’ tabs
Users can browse through Patient’s scans in top 1/3 panel of the tabs in the Scan Database and view and sort by “Patient Name”, “Patient ID”, “Birth Date”, “Sex”, “# of Studies”, “Last Study Date”, and “Date Added”. Where scans have been anonymised, ‘N/A’ is used.
Users can rename the “Patient Name” by double clicking on the Patient name field anywhere that the field occurs in the Scan Database
Users can browse through all ‘Studies’ associated with a patient in the 2/3 panel of the tabs in the Scan Database and view and sort by “Study Date”, “Study ID”, “Study Description”, “# of Series in that study”, and “Date Added”
Users can rename the “Study Description” by double clicking on the Study Description field in the Scan Database in the 2/3 panel in each tab
Users can browse through all ‘Series’ associated with a patient’s particular study in the ‘Series’ panel of the Scan Database once they’ve selected a particular Study. They can view the series and sort by “Series #”, “Series Description”, “Modality of Scan”, “Count – # of images in the scan”, and “Date Added”
Users can hover over a thumbnail in the ‘Series’ panel in the Scan Database to see a scrolling preview of the scan in the plane of acquisition
Anonymise DICOM series by clicking on the “Anonymise” icon next to a series in the Scan Database
Remove scans and models from the Scan Database by clicking the “Delete” icon next to a patient/study/series and/or model in the Scan Database
Load DICOM & NII files into the program from removable media such as CD/USD by clicking ‘Local’ tab and then “Load from Removable Media” and browsing to the folder containing DICOM or NII files
Load DICOM & NII files which have been sent via Medical File Transfer Protocol from the Scan Database by clicking on the ‘MFTP’ tab and viewing any received files
Load DICOM & NII files into the program from a local Picture Archiving and Communications System through the Scan Database (with initial configuration settings entered in ‘Global Settings’) by clicking on the ‘PACS’ tab and viewing/opening PACS files from there
Load DICOM & NII files into the program from a cloud-based Picture Archiving and Communications System (PACS) through the Scan Database (with initial configuration settings entered in ‘Global Settings’) by clicking on the ‘PACS’ tab and viewing/opening cloud PACS records/files from there.
Load/Retrieve and view radiological reports from local directory linked to a patient/study or series in the Scan Database by clicking on the Patient Name in the ‘Local’ tab, then the relevant study and finding the report in the ‘Series’ 3/3 panel.
Load/Retrieve and view radiological reports from local PACS linked to a patient/study or series in the Scan Database by clicking on the Patient Name in the ‘PACS’ tab, then the relevant study and finding the report in the ‘Series’ 3/3 panel.
Load/Retrieve and view radiological reports from cloud-based PACS linked to a patient/study or series in the Scan Database by clicking on the Patient Name in the ‘PACS’ tab, then the relevant study and finding the report in the ‘Series’ 3/3 panel.
Load a Session linked to a series in the Scan Database to import particular states, markups and edits made to the original DICOM file by clicking on a Series. If a session(s) is saved to that series, a modal popup appears and gives the option to choose from a list of sessions associated to that Series.
Load Computer Aided Design files into the software from a local directory through the Scan Database by clicking on the ‘3D Models’ tab, clicking “Add Model” and browsing to a folder containing .STL, .PLY. OBJ or .FBX models. 
Load Computer Aided Design files into the software from MFTP through the Scan Database by clicking on the ‘MFTP’ tab and filtering by “3D Models”
Create/save a Session relating to a particular scan to the Scan Database with a ‘Session Name’ and Notes by clicking ‘Save’ in the top-bar; saved states include but aren’t limited to 3D Model position, HU density values of upper/lower thresholds, brightness, contrast and opacity settings, 3D slicing positions, measurements, annotations and 2D view positions/slices.
Create/save a Session relating to a particular scan to the Scan Database with a ‘Session Name’ and Notes upon Exit or at particular event-based milestones; saved states include but aren’t limited to 3D Model position, HU density values of upper/lower thresholds, brightness, contrast and opacity settings, 3D slicing positions, measurements, annotations, 2D view positions/slices, segmentation settings, and Computer Aided Design file settings/parameters and positions.
Upon loading of a scan, view pertinent scan information such as Patient Name (N/A if anonymised), Date of Birth, Series name and slice thickness / modality in the “Scan Information” panel in bottom left.
User can share a file from the top menu. Spawns a modal popup that steps user through saving, anonymisation, compression and exporting (via email or via MFTP) process.
User can share a 3D model from the ‘3D Models’ tab by clicking on a share icon next to each 3D model in the list / grid layout in the tab. Spawns a modal popup that steps user through sending the model via email or via MFTP.
User can share a session (and associated scan) by clicking through the “Patient”, “Studies” and “Series” panels and then clicking on a “Sessions ICON” next to the series. This opens a popup with a list of the sessions associated with the scan and their date of creation/last modified and a share icon next to each session. If a user clicks to share a session, they can choose to anonymise the series and/or toggle on/off what attributes are part of the shared session prior to sharing via MFTP.
User can share radiological report(s) by browsing through the “Scan Database” to a specific Study and then clicking on the Share icon next to the report in the list. A dialog box opens and provides the ability to send via email or MFTP and requests the user to check a box stating they have permission to share it.
User can export file(s) from MFTP, PACS, Cloud PACS to their local directory directly from the tabbed interface by clicking into “MFTP”, “PACS” tabs and then clicking on an Export/Download Icon next to the chosen Study or Series. A disclaimer is shown in a dialog box along with option to anonymise scan prior to Export/Download.
User can export 3D model(s) to their local directory directly from the “MFTP”, “3D Model” tabs and then clicking on an Export/Download Icon next to the chosen 3D Model. 
User can export a radiological report to their local directory from the “MFTP” and “PACS” tabs by clicking on an Export/Download Icon next to the desired report.
User can save their current session / scan by clicking on the “Save” button in the top bar as per #30.

Visualisation & Manipulation of Medical Scans and Computer Aided Design Models

Users can collapse the LHS and RHS panels to maximise the main view and then re-expand the side panels individually for the additional views and controls.
Visualise CT/MRI/PET scans in 2D plane of acquisition and scroll through images/slices using sliders and/or scroll wheel/trackpad in the smaller 2D views in RHS panel or in the full-screen view
Visualise CT/MRI/PET scans with 2D multiplanar reconstruction and scroll through each 2D plane using sliders and/or mouse scroll-wheel / trackpad in the smaller 2D views in RHS panel or in the full-screen view
Users can visualise where the cursor is in one-plane across other 2D planes with planar cross hairs to correlate the cursor position in different planes.
Visualise CT/MRI/PET scans as a single 3D volumetric model with ability to zoom, pan and rotate using a mouse and keyboard inputs
Users can edit the sensitivity of the Panning and Rotation by navigating to “Settings – General” and using the “Pan Sensitivity” and/or “Rotation Sensitivity” sliders to personalise the level of sensitivity. 
Adjust the Hounsfield range / density values to expose various anatomical structures in the 2D & 3D views using a slider tool located in the LHS ‘Display’ panel controlled by a mouse as the input
Using a mouse and keyboard, click on the text fields above the Hounsfield / Density slider in the LHS ‘Display Panel’ and click then type to enter precise density values to expose desired anatomical structures
Utilise preset density value ranges to visualise certain anatomical structures (CT scans only) such as skin, muscle and bone with icons to toggle these ranges on and off
Automatic scale (to automatically set HU range to display first recognisable object)
User can click on the ‘Reset’ icon above the Density slider (#49) to reset the Hounsfield / Density values to their initial automatically scaled position
Adjust the brightness of the scan (happens to both 2D & 3D views) using a slider tool located in the LHS ‘Display’ panel controlled by a mouse as the input
Adjust the contrast of the scan (happens to both 2D & 3D views) using a slider tool located in the LHS ‘Display’ panel controlled by a mouse as the input
Adjust the opacity (happens to both 2D & 3D views) using a slider tool located in the LHS ‘Display’ panel controlled by a mouse as the input
Input precise Brightness, contrast and opacity values in addition to the slider input by clicking on the text field next to each slider and using a keyboard to enter a precise value
User can click on the ‘Reset’ icon above the Brightness, Contrast and Opacity sliders (#54-56) to reset the Brightness, Contrast and Opacity values to their default positions
Slice’ into the 3D model in the three 2D planes; Sagittal, Coronal and Transverse using slider tools located in the LHS ‘Display’ panel controlled by a mouse as the inputs
Lower’ & ‘Upper’ slice values are represented in small boxes above each 2D plane slider for #59 and can be entered manually for precise control.
User can ‘crop’ a scan to create a new DICOM or NIFTI scan by moving the Sagittal, Coronal, and/or Transverse sliders or entering precise values as per #56 and then clicking on a button in the Display Panel called “Crop”. This spawns a modal popup that allows the user to save the newly cropped scan. Upon exit from the software or when saving, the User MUST save the scan as a new series in .DCM or .NII format. 
User can click on the ‘Reset’ icon above the Sagittal, Coronal and Transverse sliders (#59) to reset the scan to its default slicing position
Toggle on/off hyper-realistic colour rendering with lighting, shadows etc. based on density value ranges (CT scans only) by enabling the “Enable Colour Rendering” button at the bottom of the “Display” panel on the LHS. Only works with CT scans and compatible hardware.
Orientate the 3D model into standard viewing angles using a Navigation Cube that operates similar to Computer Aided Design programs
Users can edit the size of the Navigation Cube by navigating to “Settings -> Navigation Cube Settings” and using the slider to increase or decrease the Navigation Cube size. 
Capture screenshots of the ‘raw’ (without markups or annotations) 3D volumetric model by clicking on the “Camera icon” next to the Navigation cube. Saves image to a standard file directory location such as ‘Downloads’  or a custom file path/destination can be set in “Global Settings -> Media”.
Capture screenshots of the 3D volumetric model with annotations & measurements by clicking on the “Camera icon” next to the Navigation cube. Saves image to a standard file directory location such as ‘Downloads’  or a custom file path/destination can be set in “Global Settings -> Media”.
Capture screenshots of the 3D volumetric model with annotations, measurements and CAD model positions and segmentations by clicking on the “Camera icon” next to the Navigation cube. Saves image to a standard file directory location such as ‘Downloads’  or a custom file path/destination can be set in “Global Settings -> Media”
Capture screenshots of the ‘raw’ (without edits) scan images in a particular 2D plane by clicking on the small camera icon next to the 2D view on the right hand side panel. Saves to a standard file directory location such as ‘Downloads’ or a custom file path/destination can be set in “Global Settings -> Media”.
Capture screenshots of the 2D scan images in a particular 2D plane with annotations & measurements shown by clicking on the small camera icon next to the 2D view on the right hand side panel. Saves image to a standard file directory location such as ‘Downloads’  or a custom file path/destination can be set in “Global Settings -> Media”.
Capture screenshots of the 2D scan images in a particular 2D plane with annotations, measurements, segmentation masks and CAD models shown by clicking on the small camera icon next to the 2D view on the right hand side panel. Saves image to a standard file directory location such as ‘Downloads’  or a custom file path/destination can be set in “Global Settings -> Media”.
Capture video recordings of the 3D view by clicking on ‘Record’ in the “Media” panel in the LHS panel with/without UI + markups recorded (as chosen in the Global Settings) and with/without Microphone recording (as chosen in “Media” panel in LHS).
Capture video recordings of individual 2D views by clicking and holding the Camera Icon next to a 2D view in the RHS panel until the Camera Icon turns red. User can then interact with the 2D scans and record until clicking on the Red Camera Icon again.
Fullscreen a particular 2D plane by clicking on the [ ] icon on the right hand panel next to the view. When a 2D view is full-screened, a slider appears at the bottom in the middle for scrolling through the images
Rotate a 2D view/plane by 90 degrees clockwise at a time by clicking on the ‘Rotate Icon’ next to a particular 2D view on the RHS panel. Rotation can also be conducted when the 2D view is fullscreened by clicking on the corresponding ‘Rotate icon’
Orientate the 2D views and flip them horizontally by clicking on the “Flip Horizontally Icon” on the right-hand side panel corresponding to a particular 2D view.
Orientate the 2D views and flip them vertically by clicking on the “Flip Vertically Icon” on the right-hand side panel corresponding to a particular 2D view.
Inverse the direction in which a user scrolls through the series of 2D images by clicking on the ‘Image Stack Icon’ on the RHS panel
View the current image number in the Tranverse, Coronal and Sagittal planes represented over the total images in that plane. I.e. 84/512 in the Coronal plane or 280/620 in the transverse plane)
Rotate the camera/first person view of the 3D model, rather than the model itself, to view internal structures from a single position (360* immersive view) by clicking on……

Measurements & Annotations

Visualise and edit annotations in the scan in 2D views (DOT + label in 2D views). Edit information by double clicking on the respective Annotation in the filterable Markup list of Annotations and Measurements located in the ‘Measure’ panel on the LHS panel. Clicking and holding on the DOT in the 2D views creates a dialog box with the 3D spatial coordinates, the Title and a =>200 character description and ability to drag the annotation to a new location.
Visualise annotations in the scan in 3D view (Dotted line and label in 3D view) – READ ONLY ACCESS. Annotations can be provided from practitioners in Pro / Surgical to patients in 3Dicom Lite by saving a session with annotations.
Visualise and edit annotations in the scan in 3D view (Dotted line and Title in 3D view). Clicking on the DOT in the 3D view creates a dialog box with the 3D spatial co-ordinates, the Title and a =>200 character description and ability to drag the annotation to a new location.
Toggle to select whether all annotations / measurements and markups are displayed in 2D views
Toggle to select whether all annotations / measurements and markups are displayed in 3D view
Generate Annotations in 2D views (arrow + label) which are also placed and viewed in 3D model (as a dot + label) in a light blue colour by clicking on the “Annotation” button in the “Measure” panel on the left-hand-side (LHS) and then clicking anywhere on a 2D view/plane to add a label. 
Draw/measure a straight line between two points in a 2D view by clicking on “Length” button in the “Measure” panel and then clicking and dragging between two points on a 2D image. This has the ability to toggle individual length measurements on/off in 2D and/or 3D views by ‘cycling’ through ‘2D’, ‘3D’ and ‘Hidden’ options by clicking on the relevant measurement in the LHS panel list of measurements and annotations. All line measurements/drawings are coloured light green. 
View any/all straight line measurements/drawings in 2D and 3D views loaded from previous sessions or shared by another user of 3Dicom
Draw/measure a closed polygon in a 2D view by clicking on “Polygon” in the “Measure” panel and creating multiple points in a 2D view by clicking. This has the ability to toggle area & perimeter measurements on/off in 2D and/or 3D views by cycling through ‘2D’, ‘3D’ and ‘Hidden’ options by clicking on the relevant measurement in the LHS panel list of measurements and annotations. All polygon measurements/drawings are coloured bright red.
View any/all closed polygon measurements/drawings in 2D and 3D views loaded from previous sessions or shared by another user of 3Dicom
Draw/measure a circle in a 2D view by clicking on the “Circle” button in the “Measure” panel and click and drag on a 2D image. This has the ability to toggle diameter, circumference and area measurements on/off in 2D and/or 3D views by cycling through ‘2D’, ‘3D’ and ‘Hidden’ options by clicking on the relevant measurement in the LHS panel list of measurements and annotations. All circle measurements/drawings are coloured dark blue.
View any/all circle measurements/drawings in 2D and 3D views loaded from previous sessions or shared by another user of 3Dicom
Measurement of a single angle on a 2D plane by clicking on the “Angle” button in the “Measure” panel and then clicking three times on a 2D plane to create an origin point, point of incidence and a final point. The resultant angle is then displayed overlaid on the 2D plane near the point of incidence. The 2D angle tool has the ability to toggle angle measurement on/off in 2D and/or 3D views by cycling through ‘2D’, ‘3D’ and ‘Hidden’ options by clicking on the relevant measurements in the LHS panel list of measurements and annotations. All angle measurements/drawings are coloured bright orange.
Measurement of COBB angle on a 2D plane
View any/all COBB angle measurements/drawings in 2D and 3D views loaded from previous sessions or shared by another user of 3Dicom
Create 3D measurement of length by clicking on the “Length” button in the “Measure” panel and adding an origin point on a selected 2D slice/image in one plane and then adding a second point on a separate 2D slice/image in the same plane. This measurement is for the resultant 3D vector between the two points. The drawing and measurement is coloured light green.
View any/all 3D length measurement in the 3D view
Toggle visualisation of 3D measurements on/off
Create a 3D angle measurement by clicking on the “Angle” button in the “Measure” panel, clicking on a point on a 2D image in a particular plane to create an origin point, then scroll through images on the same plane and create a second point of incidence before finally creating a third and final point on another 2D image in the same 2D plane. The resultant 3D angle is coloured bright orange.
View any/all 3D angle measurement(s) in the 3D view
Toggle visualisation of 3D angle measurements on/off
View labels and measurements of any/all drawings, measurements and/or annotations as a list in the “Measure” panel with the ability to filter which measurements are displayed in the list. 
Delete any annotations, drawings and/or measurements created relevant to that user’s access level as described above from #83 – 102 by using the Bin icon next to any of the measurements / annotations in the list in the LHS “Measure” panel or by clicking on a measurement/annotation in a 2D view and using the “Delete” key on the keyboard.
Rename any annotations, drawings and/or measurements created relevant to that user’s access level as described above from #83- 102 by double clicking on any of the measurements / annotations in the list in the LHS “Measure” panel.
Hover over any measurement in the list of measurements / annotations in the LHS “Measure” panel or on the visual representation of the measurement in a 2D plane to spawn a dialog box just below and to the right of the cursor with the finer details of the measurement and/or annotation

Media Recording

Users can acquire images & video through the methods detailed in #66 – 73 above based on their User Level permissions
Users can view an in-application “Media Gallery” in the “Media” panel on the LHS which contains images and videos acquired of the loaded Scan in the current, and/or previous, 3Dicom session.
Users can click on a thumbnail in the “Media Gallery” to open an in-application preview of the images/videos. Users can also click on a ‘Bin’ icon in the Media Gallery to delete images / videos acquired during the current session. Users can share the images via email directly from the Media Gallery.
Users can click on the “Open File Location” button in the LHS “Media” panel to browse directly to the location where images and video acquired in 3Dicom is stored. They can also do this in the “Settings -> Media” tab.
Users can edit where the image and video files are saved to by accessing the “Settings -> Media” tab and clicking “Change Save Location”
Users can select whether or not measurements, annotations, segments and all other ‘markups/edits’ are displayed in screenshots / videos by toggling the “Markups in Media” setting located in “Settings -> Media” tab.  Set to False and uneditable for 3Dicom Patient users.
Users can select whether or not to display the User Interface (side panels etc.) in screenshots / videos by toggling the “UI Recording” setting located in “Settings -> Media” tab. Set to False and uneditable for 3Dicom Patient users.
Users can select their preferred Microphone and Speakers from the “Microphone & Speaker” settings located in “Settings -> Media” tab and selecting from the available audio input/outputs.

Research

Users can view all of the DICOM tags from the loaded Scan / Session and sort them from A-Z and search in a scrollable list. User can expand / collapse this scrollable list for additional space in the panel.
Users can fully anonymise DICOM tags and save as a new series.
Users can convert the DICOM to .NII format by clicking on a button located in the Research panel of the LHS UI that says “Convert DICOM”. This spawns a modal popup which provides the User with the ability to choose the desired output format via a drop-down list, the destination folder and any other parameters. For Surgical users, the output type can be changed to .NRRD or .MHD as per #155 & 156
Users can convert the DICOM to .NRRD format by clicking on the same button as #153 that says “Convert DICOM”. This spawns a modal popup which provides the User to choose the desired output format via a drop-down list, the destination folder and any other parameters. 
Users can convert the DICOM to .MHD format by clicking on the same button as #153 that says “Convert DICOM”. This spawns a modal popup which provides the User to choose the desired output format via a drop-down list, the destination folder and any other parameters. 
User can bulk export the raw DICOM to .JPG in the X, Y, Z planes as one of the drop down options detailed in #156.
User can bulk export the raw DICOM to .PNG in the X, Y, Z planes as one of the drop down options detailed in #156.
Users can bulk export binary masks in the X, Y, Z planes by clicking on the same “Bulk Export Images” button detailed in #156 and then selecting ONE already created segment as the mask to be used as part of the modal popup flow. Binary masks can be exported as .TIFF, .JPG, .PNG, the mask is always white and background/all else is black, and it can be selected to be exported in any/all of the X, Y, Z planes.
Users can bulk export multi-class masks in the X, Y, Z planes using multiple selected segments as the masks with same functionality as #159 but with multiple masks shown. Masks can have different colours but background/anything else is always black.
User can access a standard Hounsfield Histogram in the bottom right of the Research panel in LHS UI and adjust the windowing values with an upper & lower slider on the Histogram. The Histogram can be viewed in a larger view for screenshots with a modal ‘full-screen’ mode along with additional Quantitative Analysis (Mean, Median, Lowest, Highest etc.) about the Hounsfield values, greyscale gradients etc.
Users can access specific research-focused Python libraries and apply their functionality through modal popups (PyRadiomics etc.) (https://pythonrepo.com/tag/medical-imaging)  

Segment

The Segment panel in the LHS UI shall feature a large scrollable list area. At the top of this list shall be the “Scan Volume” which can not be renamed but shall have the ability to edit the Opacity by typing 0-100 in a small text field, with 0 being no opacity and 100 being maximum opacity. 
Users can add a segment to the list of segments by clicking on a “+” icon at the bottom of the list, this then creates a new segment in the list which has name of “Segment n+1” and is allocated a ‘new’ colour. 
Users can remove a segment from the list of segments by clicking on the segment to highlight it, then clicking on a “-” icon at the bottom of the list. This spawns a dialog box saying “Are you sure you want to remove this segment? Yes/No” 
To the left of the Scan Volume shall be an icon of a 3D cube. To the immediate left of all other segments in the segment list of #165 shall be a square containing a colour. Clicking on this square will provide users with a drop-down list of preset colours for anatomy (https://www.slicer.org/wiki/Slicer3:2010_GenericAnatomyColors) and an ever-present option at the top of the list called “Custom” which allows the User to create a colour from a RGBA mixing panel.
Users can rename a segment by double-clicking on the Segment name. This then creates a white text field which can be typed into. Hitting “Enter” or clicking out of the text field closes the text field and sets the segment name to whatever is in the text field.
Users can see the volume of the segment to the immediate right hand side of the segment name inside of brackets (30 mm3) and displayed as mm3. 
Users can edit the opacity of a segment by clicking on a square to the right of the name/volume which contains a number from 0-99. By editing this number, the Opacity of the segment can be changed to a specific value between 0 & 99 and visualised in the 2D and 3D views. 
To the left-hand most side of a segment in the segment list shall be an ‘Eye’ icon which can be clicked to toggle between the segment being visible in the 2D /3D views or not shown.
Users can select a single segment by clicking on a Segment in the segment list once. This activates the segmentation tools located below the list which are further detailed in #180 – 200.
Users can select multiple segments by holding Shift and left clicking on multiple segments. Users can also remove segments from the multiple selection by continuing to hold Shift but clicking on the desired segment with a right click. 
If no segments are selected in the segment list, Users can hover over segment masks in the 2D and/or 3D views and an outline appears and an overlaid label with the name & volume of the segment.
Users can merge segments by selecting multiple segments as per #174 and then clicking on a button at the bottom of the segment list next to the “+” and “-” buttons that has a ‘merge’ icon. A dialog box appears stating “Merging segments can’t be undone. Do you want to proceed? Yes/No”. The original segments are combined into a new segmented called “Merged Segment n+1” and original segments are removed from the segment list.
Users can duplicate a segment(s) by selecting one or more segments in the list and clicking on a button at the bottom of the segment list to the right of “Merge” that has a duplicate icon. All segment attributes such as colour, visibility, opacity, HU threshold ranges etc. are copied to a new segment(s) which is named “{Original Segment Name} + “Copy””
Users can undo / redo recent changes to segments only by clicking on the “Undo” / “Redo” icon buttons at the bottom of the segment list to the right of the Duplicate button. Users can also use global Undo/Redo with Ctrl/Cmd + Z, Ctrl/Cmd + Y.
Show Segments in 3D. Located under the segment list shall be a toggle that allows Users to toggle on/off to show visible segments in the 3D view in addition to the 2D views. By default, this should be turned off. Additionally, there should be a tooltip or text below this button that advises users that 3D viewing may slow the software.
Located under the segment list shall be a toggle that allows Users to toggle on/off to show only selected segments in 3D view OR show all visible segments in 3D view.
User should be able to toggle on/off a Hounsfield Pointer using a button/toggle located under the segment list. Toggling this on results in a dialog box appearing to the lower-left of the cursor which displays the Hounsfield value of the voxel below the cursor tip.
Below the segment list and buttons shall be a horizontally tabbed interface with 8 icons being; Paint brush, Eraser, Bucket, Magic Wand, Seed, Island, Hollow, and Scissors. These icons will be greyed out if there are no segments (aside from Scan Volume) present in the Segment list or no segment(s) selected.
When a User has selected only one segment, the Paint Brush, Eraser, Bucket, Magic Wand, Island, Hollow, and Scissor icons are shown to be white (clickable) rather than greyed out. A User can click on each icon to open tabs with specific controls for each function.
When a User has selected multiple segments, all icons are greyed out with the exception of the Seed, Hollow and Scissor icons.
User can click on the Paint Brush icon to view a tab that contains a slider to define a Lower/Upper threshold to determine the HU range of voxels that can be painted/drawn on. As User changes slider values, the related voxels in the scan are highlighted with the segment colour to indicate what is editable. It also contains a slider to determine the size of the ‘brush’ which ranges from 1 voxel wide to 50 voxels wide. When User clicks and/or drags brush over a 2D view, the voxels within the defined range are coloured the same colour as that segment’s defined colour.
User can click on the Eraser icon to view a tab that contains a slider to define a Lower/Upper threshold to determine the HU range of painted/coloured voxels that can be erased. As User changes slider values, the related voxels in the scan are highlighted with the segment colour to indicate what is editable. It also contains a slider to determine the size of the ‘brush’ which ranges from 1 voxel wide to 50 voxels wide. It also contains an option/setting to erase voxels within the defined range between particular slice ranges in the X, Y, Z planes. When a User clicks and/or drags the eraser over a 2D view, the voxels within the defined range that have previously been coloured by any segment are erased and the ‘raw’ DICOM image/voxel is seen. 
User can click on the Bucket icon to view a tab that contains a slider to define a Lower/Upper threshold for editable HU range. As User changes slider values, the related voxels in the scan are highlighted with the segment colour to indicate what is editable. The tab also includes an option to set a range of slices in the X, Y, Z planes similar to #60 and to “Apply to all Slices”. If “Apply to all Slices” is toggled off, then clicking on a 2D view with the bucket will ‘fill’ the editable range on that slice alone. If “Apply to all Slices” is turned on, then clicking on a 2D view with the bucket icon will colour all editable voxels throughout the Scan volume and range of slices with the segment colour.
User can click on the “Magic Wand” icon to view a tab that contains a slider to define Lower/Upper threshold for editable HU range. When a User is using the ‘Magic Wand’ they can hover over an image in the 2D views and an outline is formed at the end of the cursor to create a closed path that follows the same HU/intensity value back to the starting point. The cursor can be moved around to preview different areas before clicking the left-mouse-button creates the segment and fills in the editable voxels inside of the outline.
If a User has selected multiple segments, they can click on the “Seed” icon which allows them to view a tab that contains a number of inputs/options as per https://slicer.readthedocs.io/en/latest/user_guide/modules/segmenteditor.html#grow-from-seeds 
Users can click on the Island icon to view a tab that provides them with the ability to remove artifacts from segment masks. Options include “Keep largest island”, “remove small islands (with ability to add minimum size)”. https://slicer.readthedocs.io/en/latest/user_guide/modules/segmenteditor.html#islands
User can click on the Hollow icon to view a tab that provides option to makes the selected segment(s) hollow by replacing the segment(s) with a uniform-thickness shell defined by the segment boundary. User can input a thickness value. https://slicer.readthedocs.io/en/latest/user_guide/modules/segmenteditor.html#hollow 
Users can click on the Scissors icon to view a tab that contains the same cropping functionality as #60/#61. When a User changes the slice range(s) in the X, Z, and/or Z directions, any selected segments are ‘cropped’ to fit within that range. User can then click a button that says ‘Apply’ and it crops the selected segments to fit within the new boundaries. This does not crop the DICOM itself.
In the bottom left of the Segment panel located in LHS UI shall be a full-width pill button that displays the text “Export Segment(s)” depending on whether a single or multiple segment(s) are selected. 
Clicking on the “Export Segment(s)” button shall spawn a modal popup which has multiple ‘panels/pages’ for the export flow.
Continuing on from #194. The first ‘page’ contains the list of segments with already selected segments highlighted and provides user the ability to select/deselect Segments for export. Once a User has selected all desired segments for Export, they click on ‘Next’.
Continuing on from #195, when a User clicks ‘Next’ if any of the segments contain a break (a missing slice in any view between two other slices), a warning appears and alerts them to an ‘Imcomplete segment’, which segment and what slice number if missing. If not, proceed to #199.
Continuing on from #195/#196, if a User has complete segments, clicking “Next” on the first panel of the modal popup takes the User to the second panel/page. This contains the smoothing settings. For smoothing, there shall be a button/checkbox to Enable/Disable smoothing. If smoothing is enabled, the smoothing settings are editable and consist of the smoothing lambda (which can be edited via a numerical input field) and number of iterations (default 5) which can also be edited via a numerical input field.
Continuing on from #197, the second ‘Page’/Panel of the modal popup also contains the Island removal settings. For island removal, there shall be a button/checkbox to Enable/Disable Island/Artifact removal. If enabled, islanding/artifact removal settings are editable and consist of editable minimum face/vertice threshold and a option to keep only the largest face or also allow smaller islands that are over the minimum threshold. 
Once settings in #197 and #198 are entered/selected, user can click on “Next” to proceed to the 3rd and final page/panel of the modal popup which contains the ability to browse for file destination and select the file output type from a dropdown list of “STL, OBJ or FBX”. User can then click “Apply & Export” for the export process to begin.
When the Export process is running, modal popup should close and there should be a progress / loading wheel in the right hand side of the top bar along with text saying “Exporting Segments”. There should also be an “Cancel” button next to this to stop the processing if it locks up the software or is indefinitely processing.

Design

User can access a panel in the LHS UI called “MCAD” which shall feature a half-height scrollable list section and a number of controls both below the list and in the main 3D view. Whilst in the MCAD panel, the RHS UI containing the 2D views is hidden resulting in a larger screen area for the 3D visualisation area.
At the top of the scrollable list shall be the “Scan Volume” which can not be deleted or renamed but shall have the ability to edit the Opacity by typing 0-100 in a small text field, with 0 being no opacity and 100 being maximum opacity. 
Users can add CAD model(s) to the list of CAD models by clicking on a “+” icon at the bottom of the list, this then allows the user to add new CAD model(s) to the list by browsing to a local file directory and selecting a compatible CAD file(s). These are named in the list depending on their file name (minus extension) and are allocated a colour unless they already have color data. By default, when models are added they are slightly indented compared to ‘Scan Volume’ to show they’re part of the scene/collection.
Users can also add CAD model(s) by opening the “Scan Database” from the top bar and then navigating to “3D Models” and clicking on a file to add it to the list in the MCAD panel and have it open in the MCAD view. By default, when models are added they are slightly indented compared to ‘Scan Volume’ to show they’re part of the scene/collection.
Users can remove CAD model(s) from the list of CAD models by selecting model(s), then clicking on a “-” icon at the bottom of the list.
To the left of the Scan Volume shall be an icon of a 3D cube. To the immediate left of all other CAD models in the list shall be a square containing a colour. Clicking on this square will provide users with a hexagonal colour picker to colour the CAD model whilst in 3Dicom to differentiate them.
Users can rename a CAD Model in the list by double-clicking on the CAD Model name. This then creates a white text field which can be typed into. Hitting “Enter” or clicking out of the text field closes the text field and sets the name to whatever is in the text field.
Users can see the volume of the CAD model to the immediate right hand side of the CAD model name inside of brackets (30 mm3) and displayed as mm3. 
Users can edit the opacity of a CAD Model by clicking on a square to the right of the name/volume which contains a number from 0-99. By editing this number, the Opacity can be changed to a specific value between 0 & 99 and visualised in the 3D view.
To the left-hand most side of a CAD Model in the list shall be an ‘Eye’ icon which can be clicked to toggle between the CAD Model being visible or not regardless of opacity.
Users can indent/unindent CAD Models in the list by dragging and dropping the CAD Models by clicking, holding and dragging them. Moving a selected CAD model on top of another CAD model in the list will indent the selected model and make it a child of the other model. Users can always select child models and drag them back out to be unindented. Similar to WP Menu
Users can select a single CAD Model by clicking on a CAD Model in the CAD Model list once. 
Users can select multiple CAD Models by holding Shift and left clicking on multiple CAD Models. Users can also remove CAD Models from the multiple selection by continuing to hold Shift but clicking on the desired CAD Model with a right click. 
Selecting/modifying the visibility and/or opacity of a “Parent” CAD model will select/move all Child models of that parent whereas selecting a Single child model will select/move/hide/show only the selected child models
Users can merge CAD models by selecting multiple CAD Models as per #214/215 and then clicking on a button at the bottom of the CAD Model list next to the “+” and “-” buttons that has a ‘merge’ icon. A dialog box appears stating “Merging models can’t be undone. Do you want to proceed? Yes/No”. The original Models are combined into a new CAD Model called “Merged Model n+1” and original CAD models are removed from the segment list. This is different from grouping as its actually combining them into one new STL/OBJ file not just making them move relational to one another.
Users can group CAD models by selecting multiple CAD Models as per #214/215 and then clicking on a button at the bottom of the CAD Model list next to the “+” and “-” buttons that has a ‘group’ icon. An icon appears next to grouped CAD Models to indicate they’re part of a group and they move/rotate etc. as though they’re one component (similar to #216 but parent Models can be grouped). Models can also be ungrouped.
Users can duplicate a CAD Model(s) by selecting one or more CAD Models in the list and clicking on a button at the bottom of the CAD Model list to the right of “Merge” that has a duplicate icon. All attributes such as colour, visibility, opacity, position and Hierachy etc. are copied to the new CAD Model(s) which is named “{Original CAD Model Name} + “Copy””
Users can undo / redo recent changes to CAD Models only by clicking on the “Undo” / “Redo” icon buttons at the bottom of the CAD Model list to the right of the Duplicate button. Users can also use global Undo/Redo with Ctrl/Cmd + Z, Ctrl/Cmd + Y.
Located under the CAD Model list shall be a toggle that allows Users to toggle on/off to show only selected CAD Models in 3D view OR show all visible CAD Models in 3D view.
Holding Shift + Left Mouse Click and Drag results in the user moving the Camera around the 3D space with the 3D models (including Scan Volume) not being moved. This allows for the User to view the Scan Volume / 3D models from any angle without rotating the Scan Volume/CAD Models themselves. 
If a User has selected a single CAD model (or Scan Volume), the 3D environment remains ‘still’ and only the selected model moves relative to the 3D environment and other CAD models/Scan Volume with the movement being based around that sole CAD model’s volumetric center.
If a User has selected multiple CAD models and/or Scan Volume, then the selected models all move together relative to the 3D environment and other unselected CAD models / Scan Volume with the movement being based around a central point between the volumetric centres of all the selected CAD Models. 
Users can select CAD Model(s) by clicking on Visible Models in the 3D view or any model in the CAD Model list and then view a CAD-style gizmo containing the rotation sphere, 3 axis movement arrows and 3 axis scale arrows. Clicking and dragging on any of the 3 axis movement arrows allows a Users to move the model back and forth along that axis. Additionally, the User can also click on the intersection of the 3-axis at the centre point to move the model freehand in any direction. 
Users can use the rotation sphere to rotate selected CAD models around the volumetric centre point by clicking and dragging on either of the rotation directions (azimuth, elevation). 
Users can scale selected CAD Model(s) using the 3 axis scale arrows in the CAD-style gizmo. Using an outer-most arrow scales the model equally in all directions, whereas using a slightly inboard scale arrow scales the model only in that respective plane.
Users can view a transform panel on the LHS panel under the list which contains the spatial location of the volumetric centre of the selected CAD Model(s) in the X, Y, Z planes along with rotational information, scale compared to original file and the total volume of the selected CAD Model(s). 
Users can use the transform panel to enter specific coordinates for movement, degrees (for rotation) and % for scale. They can also toggle between Global and Local coordinates.
Users can click on a button in the transform panel to lock the selected CAD model(s) to a particular position in the global co-ordinates. Locked CAD model(s) are locked to the Scan Volume and can not be interacted with (aside from changing colour, opacity and visibility) until unlocked in the Transform panel. Locked models have a Lock icon next to their name/volume in the CAD Model list. 
Users should be able to view icons for additional camera controls and settings underneath the Navigation cube to assist them in effectively visualising both the CAD Models and their relationship to the Scan Volume in 3D space. These icons should be vertically stacked and be informed by internal testing and best-practice Camera controls/settings in CAD Programs. 
As part of #231, Users should have the ability to toggle on/off the ability to lock a particular distance from the Volumetric centre of a selected CAD Model(s) whilst panning / rotating camera view in any direction. 
Users should have the ability to set numerous off screen controls such as mouse settings and hotkeys under “Off screen controls / hotkeys” for the MCAD functions within the full list of hotkeys as per #261.
Users can NOT use tools from the Measure panel to make measurements whilst in the MCAD view, however if CAD Model(s) 2D slices can be accurately displayed in the 2D views whilst a User is in the “Measure” panel, then the standard measurement tools can be used to make temporary measurements. Measurements of CAD Model(s) 2D ‘masks’ should only be temporal to account for if a 3D model is moved in the MCAD panel, the measurement would no longer be accurate / relevant in the Measure panel. 
As part of the icons below the navigation cube (as per #231), Users should be able to click on a “Ruler” icon to make 3D point-to-point measurements in MCAD only (disclaimer to state that it’s indicative only). Very similar to the measurements in VSP. 
Located in the bottom of the “MCAD” panel shall be a button that says “Reset all”. Clicking on the button shall spawn a dialog box that says “Resetting all will revert all changes to all current CAD models, do you want to proceed? Yes/No”. Clicking the button shall revert all changes made in the current MCAD session.
Located in the bottom of the “MCAD” panel shall be a button that says “Quick Export to Virtual Surgical Planning (VSP)”. If a User clicks on this, it spawns the usual Save panel which spawns same modal popup save function as #30 but also an additional page for the User to share the entire session or selected models, CAD measurements (as per #235) and other attributes direct to VSP by sharing it with themselves via MFTP so it appears in the Oculus Quest 2. 
Located in the bottom half of the “MCAD” panel shall be a button that says “Save CAD Models”. If a User clicks on this button, it should provide them with a modal popup that allows them to the currently selected CAD Model(s) to a local Directory and/or add the CAD Model(s) to the “3D Models” list in the Scan Database for easy loading in the future. NOTE: This save feature saves/exports the local geometry/size of the models but not the global position settings etc. to Save the MCAD session and/or 3Dicom session, the User should click on “Save” in the top bar as per #30 & #31.

General Settings

Users can view short GIFS, silent videos and step-by-step guides by hovering over the titles of major features / functions in the side panels of the software
Users can access tooltips by hovering over Features / Functions in the software and titles of buttons/panel titles etc. throughout the User Interface.
Users can toggle tooltips on/off by navigating to “Settings -> General” and toggling on/off the “Enable Tooltips” setting.
Users can reset their installation of 3Dicom and clear the “Scan Database” of all scans by navigating to “Settings -> General” and clicking on “Clear Cache”. They will be prompted to type “DELETE” into a text field to verify and then they can click Apply. 
Users can create hotkey shortcuts using either individual mouse and keyboard inputs or a combination of mouse and keyboard inputs. These hotkeys can be configured by the User in the Global Settings panel under the “Controls” tab
Users can edit their Media settings in the Settings panel under the “Media” tab as per #114 – 118. 
Users can edit their Hotkey combinations in “Settings -> Hotkey” tab.
Users can click on the ‘Help’ icon in the bottom left of the software to spawn a large dialog box which contains the level and version of the software and a link to the most recent Instructions for Use manual in PDF. Underneath this, there will be a form which they submit direct to “Freshdesk”. This is Singular Health’s CRM for customer feedback and post-market surveillance. The user will then be emailed directly by a Singular Health representative.
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