added workflow figure

moved all figures into common location
BrainLesion · Nov 16, 2023 · 25bccd0 · 25bccd0
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diff --git a/README.md b/README.md
@@ -10,9 +10,9 @@ The package provides 3 core modules:
 
 1. Instance Approximator: instance approximation algorithms in panoptic segmentation evaluation. Available now: connected components algorithm.
 1. Instance Matcher: instance matching algorithm in panoptic segmentation evaluation, to align and compare predicted instances with reference instances.
-1. Panoptic Evaluator: Evaluation of panoptic segmentation performance by evaluating matched instance pairs and calculating various metrics like true positives, Dice score, IoU, and ASSD for each instance.
+1. Instance Evaluator: Evaluation of panoptic segmentation performance by evaluating matched instance pairs and calculating various metrics like true positives, Dice score, IoU, and ASSD for each instance.
 
-<!-- ?TODO: add module figure? -->
+![workflow_figure](https://github.com/BrainLesion/panoptica/blob/main/examples/figures/workflow.png)
 
 ## Installation
 
@@ -28,7 +28,7 @@ All use cases have tutorials showcasing the usage that can be found at [BrainLes
 
 ### Semantic Segmentation Input
 
-<img src="https://github.com/BrainLesion/panoptica/blob/main/examples/spine_seg/semantic/fig_dark.png?raw=true" alt="semantic_figure" height="300"/>
+<img src="https://github.com/BrainLesion/panoptica/blob/main/examples/figures/semantic.png?raw=true" alt="semantic_figure" height="300"/>
 
 Although for many biomedical segmentation problems, an instance-wise evaluation is highly relevant and desirable, they are still addressed as semantic segmentation problems due to lack of appropriate instance labels.
 
@@ -38,7 +38,7 @@ Modules [1-3] can be used to obtain panoptic metrics of matched instances based
 
 ### Unmatched Instances Input
 
-<img src="https://github.com/BrainLesion/panoptica/blob/main/examples/spine_seg/unmatched_instance/fig_dark.png?raw=true" alt="unmatched_instance_figure" height="300"/>
+<img src="https://github.com/BrainLesion/panoptica/blob/main/examples/figures/unmatched_instance.png?raw=true" alt="unmatched_instance_figure" height="300"/>
 
 It is a common issue that instance segementation outputs have good segmentations with mismatched labels.
 
@@ -48,7 +48,7 @@ For this case modules [2-3] can be utilized to match the instances and report pa
 
 ### Matched Instances Input
 
-<img src="https://github.com/BrainLesion/panoptica/blob/main/examples/spine_seg/matched_instance/fig_dark.png?raw=true" alt="matched_instance_figure" height="300"/>
+<img src="https://github.com/BrainLesion/panoptica/blob/main/examples/figures/matched_instance.png?raw=true" alt="matched_instance_figure" height="300"/>
 
 Ideally the input data already provides matched instances.
 

diff --git a/...s/spine_seg/matched_instance/fig_dark.png → examples/figures/matched_instance.png b/...s/spine_seg/matched_instance/fig_dark.png → examples/figures/matched_instance.png
diff --git a/examples/spine_seg/semantic/fig_dark.png → examples/figures/semantic.png b/examples/spine_seg/semantic/fig_dark.png → examples/figures/semantic.png
diff --git a/...spine_seg/unmatched_instance/fig_dark.png → examples/figures/unmatched_instance.png b/...spine_seg/unmatched_instance/fig_dark.png → examples/figures/unmatched_instance.png
diff --git a/examples/figures/workflow.png b/examples/figures/workflow.png
diff --git a/examples/spine_seg/matched_instance/fig_white.png b/examples/spine_seg/matched_instance/fig_white.png
diff --git a/examples/spine_seg/semantic/fig_white.png b/examples/spine_seg/semantic/fig_white.png
diff --git a/examples/spine_seg/unmatched_instance/fig_white.png b/examples/spine_seg/unmatched_instance/fig_white.png