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View Code? Open in Web Editor NEWmanually align specimens to annotated 3D spaces
Home Page: https://cell-locator.readthedocs.io
License: Other
manually align specimens to annotated 3D spaces
Home Page: https://cell-locator.readthedocs.io
License: Other
We currently have
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
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
Create a page with a link to the code and any other relevant information.
Is there an existing logo for the Cell Locator app or should @jtomeck create one?
What should the splash screen text say?
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
As pointed out that @dyf , they should not be displayed in red/pink but in green.
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).
Create color table with place holders for existing labels, and make sure it is available in the color table modules.
After creating the color table (See #3), there are few approaches to generate the "segments" and have them displayed in 3D:
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.
@vovythevov I suggest we disable update of reference view after user start placing an annotation
To reproduce:
=> 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.
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.
DataProbe should be updated accordingly
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.
It can probably be done when loading the file from python (or hardcoded in the metadata of nrrd file)
Values should be:
0
<max value of the volume>
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.
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.
Use "Delete" from the keyboard
To reproduce:
=> yaw/pitch/raw toggled between negative and positive values
=> volume in reslice view seems to rotate
commenting this line avoid the issue:
cell-locator/Modules/Scripted/Home/Home.py
Line 275 in 37e3623
SVG versions can be downloaded using https://drive.google.com/file/d/1eJ6-AMGsszojugjNwei6olvzkKa387sN/view?usp=sharing
Mitigation:
It's possible this has other issues as dependencies, if so, please note them.
See https://github.com/KitwareMedical/SlicerCustomAppTemplate
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