CIBC:Documentation:Seg3D:FeatureRequests:April12-07-List

This list came from Jeroen trying to use Seg3D for a real application.

Contents 1 List of issue to resolve 1.1 Continuous segmentations 1.2 Consistency in creating new layers 1.3 Multiple windows 1.4 Filter interactions 1.5 Restricting filters to selected areas 1.6 A mode for drawing contours 1.7 Being able to see layer above and below 1.8 Selecting consistent colorschemes for data 1.9 Need to be able to separately set which layers are shown 1.10 Contour only segmentation visualization

List of issue to resolve

Continuous segmentations

For segmentations to be useful in the field of bioelectromagnetism, each part of the volume needs to be assigned to a tissue type as currents flow throw the full space. Hence it is important to have every piece in the volume assigned. We could do it externally with UNU tools, but doing directly inside Seg3D would be better. However we are missing some tools to assist with this:

1. Inverting a labelmap. After segmenting out a certain area, you want the not segmented volumn to restrict the next segmentation to.
2. Flood fill: one wants the option to fill holes with a certain segmentation selection.
3. Merging, XOR, OR, AND etc on label maps.

Consistency in creating new layers

Functions like crop should create a new layer instead of altering the current one. We need to have consistent paradigm.

Multiple windows

It would be nice to have an option to launch multiple windows, so one can drag one the windows to a different monitor, so on draws segmentations in one window and renders the volume rendering the other one. So one can directly see what one is doing.

Filter interactions

The filter interactions are not clear, right now:

1. After selecting a filter tool one cannot reply it to a certain layer, without having to reselect the tool. This is frustrating.
2. The tools should give feedback: it should tell how many seed points are given, it should tell which layers will be used.
3. OK should be for ending the tool: should have a different name

Restricting filters to selected areas

1. For performance issue it would be great to restrict filters to selected areas (Does ITK permit this?)

A mode for drawing contours

Certain structures are faster segmented using contours. Drawing an inter acive spline often allows to make more continous segmentations. The other avantage is that contour drawing with a proper interface can be done relatively quikly. Being able to see the contours and keep them inside the image where one can move nodes that make up the spline around are helpful in correcting issues.

Being able to see layer above and below

Normally seeing the segmentation above and below is useful in making decisions when doing manual segmentation.

1. We could generate a mode where one sees the outlines of the layer above and below. This helps to see whether things are included in layers above or below.

1. This mode could use different color schemes for the labelmaps above and below.

Selecting consistent colorschemes for data

We need this to avoid confussion.

Need to be able to separately set which layers are shown

We need this to show segmentations in different filtered version and to overlay them side by side with different segmentations.

1. Visibility, colors etc. should be able to be set independently for each viewer window.
2. Right menu window should be window specific.
3. Locking modes between two windows, so in one we can show layer ontop and in the other one layer below.

Contour only segmentation visualization

The current visualization hides to much of the image making it hard to make good decisions when doing manual segmentation.

1. Each label in each window should be able to switch to contour mode, show segmentation, show inverse segmentation (a different pattern)

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