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It can probably be done when loading the file from python (or hardcoded in the metadata of nrrd file)

Values should be:

• min: 0
• max: <max value of the volume>

Is there an existing logo for the Cell Locator app or should @jtomeck create one?

What should the splash screen text say?

The color palette is the same as in the Allen Brand guides (#60A7E5 and #003056)

Here is an example of styled button based on the palette https://codepen.io/jradicus/pen/LgREXR?editors=1100

The current interface allows to add/remove/save/save as an annotation represented by a single fiducial. This should be changes to instead handle polyline annotation.

SVG versions can be downloaded using https://drive.google.com/file/d/1eJ6-AMGsszojugjNwei6olvzkKa387sN/view?usp=sharing

• annotate:
  

• explore:
  

• settings:
  

• opacity:
  

• thickness:
  

• new
  

• save
  

• saveas

• load

@vovythevov I suggest we disable update of reference view after user start placing an annotation

To reproduce:

1. Start application (Reference view is Coronal)
2. Create new annotation (see screenshot 1)
3. Select "Axial" reference view (see screenshot 2)
4. Click back on "Coronal" (see screenshot 3)

=> Annotation has been updated so that all points are constrained to the axial plane.

To avoid unexpected update, I suggest we disable the edit of reference view.

screenshot 1

screenshot 2

screenshot 3

Version: 0.1.0-2018-11-05

When I slice off-axis, I see strange mislabeled bands (rectangular stripes in the attached image). I don't see these when I slice on a cardinal axis. Possibly strange/incorrect interpolation?

• Ideally, tree structure
• Ability to hide and show cortical layer

Currently the brain is not oriented correctly. The orientation header in the .nrrd files used for the CCF are incorrect. Please use ASL (x=A-to-P, y=S-to-I, z=L-to-R).

• color should be hardcoded
• seeing the existing the spline point is not a problem
• thickness should be a parameter that can be set externally (ideally by updating a node property)
• visibility (and opacity?) of the polydata should be configurable (ideally by updating a node property)

• Document functions
• download: User will input the sampleid
• example of file download with progress report

Once you have chosen a slice plane axis and are moving the slice in/out of the plane, controls to set the step size and move in/out are important along using that step (e.g. via keyboard).

We currently have

• Interacting: Currently means editing point or updating annotation orientation using plane widget
• Placing: Currently means adding new point
• Scrolling: This means exploring the dataset without editing the annotation

After creating the color table (See #3), there are few approaches to generate the "segments" and have them displayed in 3D:

1. Import the label map into segmentation module and generate corresponding segments
2. Use model maker to generate the model for each "non air" label listed in the color table

First, I suggest to evaluate approach 1. Depending on the time it takes, we could look into saving the generated segmentations and bundling it with the application. If loading the segmentation file also take times, some profiling would also be needed.

Following the integration of #32, we should now hide the slider (and associated popup).

Since there is only one viewer in the application and we don't change the layout, it could be as simple as getting a reference (using python) to slicer controller widget and hiding it.

Goal: Loading an existing annotation should bring up the same "viewer settings". These includes field of view/camera settings and slice index.

• the annotation will be in its own format

• we should also store the version of the atlas, template, cell-location application in the same file

@vovythevov

• Could you investigate if there are standard for storing fiducials, custom attributes, software version, "acquisition/processing" settings etc ... may be a post on the Slicer discourse describing what we are trying to do from a high level. I think Andrey has spend a fair amount time working with standard file format.
• If there is an easy approach allowing to leverage some standard, I then suggest we use it. If not, we will role our own "format"

• Ensure the information are displayed in the DataProbe
• Eventually, customize dataprobe (or add a simple text box) to have a simpler display

DataProbe should be updated accordingly

I have created a script that generates a layer-oriented ontology instead of an area-oriented ontology.

https://gist.github.com/dyf/056095756b15a6b76dfb28558c4633da

Provide an option to switch between the default ontology and the layer ontology.

Use "Delete" from the keyboard

To reproduce:

1. Start app (no need to create an annotation)
2. Switch to Axial
3. Update reformat orientation in 3D view

=> yaw/pitch/raw toggled between negative and positive values
=> volume in reslice view seems to rotate

commenting this line avoid the issue:

As pointed out that @dyf , they should not be displayed in red/pink but in green.

• Identify parameter allowing to volume render the CCF
  • MR-default preset with Normal quality seems to work well
• Ensure volume rendering in the application is initialized with these settings

• With possibility to switch to Sagittal, Axial

Create color table with place holders for existing labels, and make sure it is available in the color table modules.

Example from connectivity.brain-map.org here:

The average_template_<resolution>.nrrd image should be the background image with the annotation/segment colors (annotation_<resolution>.nrrd) in the foreground.

For now the CCF version is available on Google drive

The idea would be organize them in https://github.com/BICCN/cell-locator where we would add a CCF-VERSIONS.md file.

Each time a new version of the CCF must be uploaded, a new entry like the following would be added to the file:

* YYYY-MM-DD: Short description
  * file1: sha256
  * file2: sha256

Then a tag named ccf-YYYYMMDD would be created and all files referenced in the new file entry would be uploaded as release assets.

See https://github.com/KitwareMedical/SlicerCustomAppTemplate

• Update SlicerCustomAppTemplate to use latest version of Slicer
• Generate skeleton using cookiecutter (Project name: CellLocator, Description: Manually align specimens to annotated 3D spaces)

Mitigation:

• Increase the size of handles
• Disable plane selection when editing point

I think adding the polyline under a transform and ensuring the transform is updated based on the location and orientation of the slice will enable this.

Tracking of the slide orientation and location should have a toggle. Then we can decide when and how to switch that toggle on/off when wiring all components in the interface

Create a page with a link to the code and any other relevant information.

It's possible this has other issues as dependencies, if so, please note them.