diff --git a/README.md b/README.md index 14ecee7..e347414 100644 --- 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. - +![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 -semantic_figure +semantic_figure 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 -unmatched_instance_figure +unmatched_instance_figure 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 -matched_instance_figure +matched_instance_figure Ideally the input data already provides matched instances. diff --git a/examples/spine_seg/matched_instance/fig_dark.png b/examples/figures/matched_instance.png similarity index 100% rename from examples/spine_seg/matched_instance/fig_dark.png rename to examples/figures/matched_instance.png diff --git a/examples/spine_seg/semantic/fig_dark.png b/examples/figures/semantic.png similarity index 100% rename from examples/spine_seg/semantic/fig_dark.png rename to examples/figures/semantic.png diff --git a/examples/spine_seg/unmatched_instance/fig_dark.png b/examples/figures/unmatched_instance.png similarity index 100% rename from examples/spine_seg/unmatched_instance/fig_dark.png rename to examples/figures/unmatched_instance.png diff --git a/examples/figures/workflow.png b/examples/figures/workflow.png new file mode 100644 index 0000000..ba57f37 Binary files /dev/null and b/examples/figures/workflow.png differ diff --git a/examples/spine_seg/matched_instance/fig_white.png b/examples/spine_seg/matched_instance/fig_white.png deleted file mode 100644 index 9923f9d..0000000 Binary files a/examples/spine_seg/matched_instance/fig_white.png and /dev/null differ diff --git a/examples/spine_seg/semantic/fig_white.png b/examples/spine_seg/semantic/fig_white.png deleted file mode 100644 index 699846c..0000000 Binary files a/examples/spine_seg/semantic/fig_white.png and /dev/null differ diff --git a/examples/spine_seg/unmatched_instance/fig_white.png b/examples/spine_seg/unmatched_instance/fig_white.png deleted file mode 100644 index 4571534..0000000 Binary files a/examples/spine_seg/unmatched_instance/fig_white.png and /dev/null differ