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Sketches

Introductory Video

7-click analysis

revision: 0.1 date: 6/13/2022

Screenshot of VTEA in action. The quickest path to interactive gating with one of the available image volumes. This sketch walks through just 7 clicks to load, segment and generate scatter-plots of cell features that can be gated and visualized in the original image volumes.
LevelIntroductory
Functionality Loading, Segmentation, Visualization
Time <5 min
ImageKidney_Cortex_Human.tif
DOI

Refining image processing

revision: 0.1 date: 6/14/2022

Screenshot of image pre-processing. This sketch demonstrates the use and application of image processing built into VTEA. The VTEA uses existing approached in ImageJ/FIJI and other ImageJ plugins.
LevelIntroductory
Functionality Loading, Image Processing, Segmentation
Time <5 min
ImageKidney_Cortex_Human.tif
DOI

Testing segmentation

Drafting release… revision: Coming soon. date: TBD

Screenshot of refining VTEA segmentation. This sketch demonstrates how to preview the effect of parameter selection and image pre-processing on segmentation.
LevelIntroductory
Functionality Loading, Image Processing, Segmentation
Time <5 min
ImageKidney_Cortex_Human.tif
DOI

Importing segmentation

Drafting release… revision: Coming soon. date: TBD

Place image here This sketch shows how to import a segmentation performed outside of VTEA, such as Cellpose, etc.
LevelIntroductory
Functionality Loading, Image Processing, Segmentation
Time <5 min
Image Kidney_Cortex_Human.tif
DOI

Supervised gating, visualization and labeling

Drafting new release… revision: 0.1 date: 4/30/2022

Supervised gating with visualization in VTEA. This sketch introduces flow cytometry-like gating and subgating and image regions-of-interest gating and visualization on the original image volume followed by manual cell instance labeling with these gates.
LevelIntroductory
Functionality Loading Datasets, Gating, Visualization, Classification
Time<5 min
ImageKidney_Cortex_Human.tif
DOI

Unsupervised classification and visualization

Planned release… revision: TBD date: TBD

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LevelIntroductory
Functionality XXXXXXXXXX
Time <X min
Image XXXXXXXXXX.tif

Neighborhood generation and analysis

Planned release… revision: TBD date: TBD

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LevelIntroductory
Functionality XXXXXXXXXX
Time <X min
Image XXXXXXXXXX.tif

Sharing results and outputs

Planned release… revision: TBD date: TBD

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LevelIntroductory
Functionality XXXXXXXXXX
Time <X min
Image XXXXXXXXXX.tif