From 621a61f6d31b9bc3c56be79c4419048b05b2cd45 Mon Sep 17 00:00:00 2001 From: Joachim Danmayr Date: Wed, 30 Oct 2024 05:40:16 +0000 Subject: [PATCH] chore: Moved --- .../classification.md | 31 ++++-------------- docs/fundamentals/images.md | 24 ++++++++++++++ .../images/image_channels.drawio.svg | 0 .../images/intersection.drawio.svg | 0 .../images/screenshot_channels.png | Bin .../images/screenshot_classification.png | Bin .../screenshot_image_channel_settings.png | Bin .../images/screenshot_intersection.png | Bin .../images/screenshot_snap_area.png | Bin .../images/screenshot_unique_name.png | Bin .../screenshot_voronoi_channel_settings.png | Bin .../images/threshold.drawio.svg | 0 .../threshold_histogram_filter.drawio.svg | 0 .../images/voronoi_building.drawio.svg | 0 .../images/voronoi_example.png | Bin .../images/voronoi_example_points.png | Bin .../images/watershed.drawio.svg | 0 docs/{analyze => fundamentals}/index.md | 3 +- .../intersection_slots.md | 0 docs/{analyze => fundamentals}/pipelines.md | 0 .../voronoi_slots.md | 0 index.md | 2 +- 22 files changed, 33 insertions(+), 27 deletions(-) rename docs/{analyze => fundamentals}/classification.md (56%) create mode 100644 docs/fundamentals/images.md rename docs/{analyze => fundamentals}/images/image_channels.drawio.svg (100%) rename docs/{analyze => fundamentals}/images/intersection.drawio.svg (100%) rename docs/{analyze => fundamentals}/images/screenshot_channels.png (100%) rename docs/{analyze => fundamentals}/images/screenshot_classification.png (100%) rename docs/{analyze => fundamentals}/images/screenshot_image_channel_settings.png (100%) rename docs/{analyze => fundamentals}/images/screenshot_intersection.png (100%) rename docs/{analyze => fundamentals}/images/screenshot_snap_area.png (100%) rename docs/{analyze => fundamentals}/images/screenshot_unique_name.png (100%) rename docs/{analyze => fundamentals}/images/screenshot_voronoi_channel_settings.png (100%) rename docs/{analyze => fundamentals}/images/threshold.drawio.svg (100%) rename docs/{analyze => fundamentals}/images/threshold_histogram_filter.drawio.svg (100%) rename docs/{analyze => fundamentals}/images/voronoi_building.drawio.svg (100%) rename docs/{analyze => fundamentals}/images/voronoi_example.png (100%) rename docs/{analyze => fundamentals}/images/voronoi_example_points.png (100%) rename docs/{analyze => fundamentals}/images/watershed.drawio.svg (100%) rename docs/{analyze => fundamentals}/index.md (80%) rename docs/{analyze => fundamentals}/intersection_slots.md (100%) rename docs/{analyze => fundamentals}/pipelines.md (100%) rename docs/{analyze => fundamentals}/voronoi_slots.md (100%) diff --git a/docs/analyze/classification.md b/docs/fundamentals/classification.md similarity index 56% rename from docs/analyze/classification.md rename to docs/fundamentals/classification.md index 1d8e1e9..aaeb5fc 100644 --- a/docs/analyze/classification.md +++ b/docs/fundamentals/classification.md @@ -5,8 +5,8 @@ The concept behind ImageC is to run pipelines containing image pre-processing an For each extracted object the origin information: image, image channel, z-stack and t-stack are stored. In Advanced, objects need to be classified for object statistics calculation and later quantification. -For classification ImageC provides the labels {guilabel}`Clusters` and {guilabel}`Classes`. -Every object is assigned to exact one cluster and class. +For classification ImageC provides the annotations {guilabel}`Cluster` and {guilabel}`Class`. +Every object is annotated with exact one cluster and one class. (clusters-and-classes)= @@ -32,27 +32,8 @@ However ImageC also allows to create own presets which can be shared with others It is recommended to use pre-defined classification presets to allow later comparison of results from different runs by different people. ::: -(image-channels)= -## Image channels +## Class hierarchy -:::{sidebar} Image plane - -An image may comprise one or more C (channels), with each channel in turn consisting of a series of T (time) stacks, and these in turn consisting of a series of Z stacks. - -The combination channel, Z stack (z) and time stack (t) is called image plane. -ImageC is able to process each image plane of an image, based on the taken project and pipeline settings. - - -```{image} images/image_channels.drawio.svg -:class: full-image -``` - -::: - - -ImageC is able to process every channel of an image based on the settings taken in the {guilabel}`Project` tab and the pipeline. -However it is possible to either process each Z stack image individually or using a projection algorithm to combine all images of a Z stack to a single stack image. -For the time stack it is either possible to analyze exact one image of a T stack or to analyze the whole time series. - -The image plane information is stored with each object extracted from that plane. -If a Z-projection is used, the Z-stack index is always assumed to be 0. +For the future it is planned to allow class hierarchies. +Class hierarchies should address the need of a more fine granular classification of objects without loosing the scope. +Statistical questions like: Give me the number of found cells! or Give me the number of found hec cells! are possible then. \ No newline at end of file diff --git a/docs/fundamentals/images.md b/docs/fundamentals/images.md new file mode 100644 index 0000000..c10ec82 --- /dev/null +++ b/docs/fundamentals/images.md @@ -0,0 +1,24 @@ +(images)= +# Images + +:::{sidebar} Image plane + +An image may comprise one or more C (channels), with each channel in turn consisting of a series of T (time) stacks, and these in turn consisting of a series of Z stacks. + +The combination channel, Z stack (z) and time stack (t) is called image plane. +ImageC is able to process each image plane of an image, based on the taken project and pipeline settings. + + +```{image} images/image_channels.drawio.svg +:class: full-image +``` + +::: + + +ImageC is able to process every channel of an image based on the settings taken in the {guilabel}`Project` tab and the pipeline. +However it is possible to either process each Z stack image individually or using a projection algorithm to combine all images of a Z stack to a single stack image. +For the time stack it is either possible to analyze exact one image of a T stack or to analyze the whole time series. + +The image plane information is stored with each object extracted from that plane. +If a Z-projection is used, the Z-stack index is always assumed to be 0. diff --git a/docs/analyze/images/image_channels.drawio.svg b/docs/fundamentals/images/image_channels.drawio.svg similarity index 100% rename from docs/analyze/images/image_channels.drawio.svg rename to docs/fundamentals/images/image_channels.drawio.svg diff --git a/docs/analyze/images/intersection.drawio.svg b/docs/fundamentals/images/intersection.drawio.svg similarity index 100% rename from docs/analyze/images/intersection.drawio.svg rename to docs/fundamentals/images/intersection.drawio.svg diff --git a/docs/analyze/images/screenshot_channels.png b/docs/fundamentals/images/screenshot_channels.png similarity index 100% rename from docs/analyze/images/screenshot_channels.png rename to docs/fundamentals/images/screenshot_channels.png diff --git a/docs/analyze/images/screenshot_classification.png b/docs/fundamentals/images/screenshot_classification.png similarity index 100% rename from docs/analyze/images/screenshot_classification.png rename to docs/fundamentals/images/screenshot_classification.png diff --git a/docs/analyze/images/screenshot_image_channel_settings.png b/docs/fundamentals/images/screenshot_image_channel_settings.png similarity index 100% rename from docs/analyze/images/screenshot_image_channel_settings.png rename to docs/fundamentals/images/screenshot_image_channel_settings.png diff --git a/docs/analyze/images/screenshot_intersection.png b/docs/fundamentals/images/screenshot_intersection.png similarity index 100% rename from docs/analyze/images/screenshot_intersection.png rename to docs/fundamentals/images/screenshot_intersection.png diff --git a/docs/analyze/images/screenshot_snap_area.png b/docs/fundamentals/images/screenshot_snap_area.png similarity index 100% rename from docs/analyze/images/screenshot_snap_area.png rename to docs/fundamentals/images/screenshot_snap_area.png diff --git a/docs/analyze/images/screenshot_unique_name.png b/docs/fundamentals/images/screenshot_unique_name.png similarity index 100% rename from docs/analyze/images/screenshot_unique_name.png rename to docs/fundamentals/images/screenshot_unique_name.png diff --git a/docs/analyze/images/screenshot_voronoi_channel_settings.png b/docs/fundamentals/images/screenshot_voronoi_channel_settings.png similarity index 100% rename from docs/analyze/images/screenshot_voronoi_channel_settings.png rename to docs/fundamentals/images/screenshot_voronoi_channel_settings.png diff --git a/docs/analyze/images/threshold.drawio.svg b/docs/fundamentals/images/threshold.drawio.svg similarity index 100% rename from docs/analyze/images/threshold.drawio.svg rename to docs/fundamentals/images/threshold.drawio.svg diff --git a/docs/analyze/images/threshold_histogram_filter.drawio.svg b/docs/fundamentals/images/threshold_histogram_filter.drawio.svg similarity index 100% rename from docs/analyze/images/threshold_histogram_filter.drawio.svg rename to docs/fundamentals/images/threshold_histogram_filter.drawio.svg diff --git a/docs/analyze/images/voronoi_building.drawio.svg b/docs/fundamentals/images/voronoi_building.drawio.svg similarity index 100% rename from docs/analyze/images/voronoi_building.drawio.svg rename to docs/fundamentals/images/voronoi_building.drawio.svg diff --git a/docs/analyze/images/voronoi_example.png b/docs/fundamentals/images/voronoi_example.png similarity index 100% rename from docs/analyze/images/voronoi_example.png rename to docs/fundamentals/images/voronoi_example.png diff --git a/docs/analyze/images/voronoi_example_points.png b/docs/fundamentals/images/voronoi_example_points.png similarity index 100% rename from docs/analyze/images/voronoi_example_points.png rename to docs/fundamentals/images/voronoi_example_points.png diff --git a/docs/analyze/images/watershed.drawio.svg b/docs/fundamentals/images/watershed.drawio.svg similarity index 100% rename from docs/analyze/images/watershed.drawio.svg rename to docs/fundamentals/images/watershed.drawio.svg diff --git a/docs/analyze/index.md b/docs/fundamentals/index.md similarity index 80% rename from docs/analyze/index.md rename to docs/fundamentals/index.md index 0915be8..040ff90 100644 --- a/docs/analyze/index.md +++ b/docs/fundamentals/index.md @@ -1,10 +1,11 @@ -# Analyze +# Fundamentals :::{toctree} :maxdepth: 3 classification pipelines +images voronoi_slots intersection_slots ::: \ No newline at end of file diff --git a/docs/analyze/intersection_slots.md b/docs/fundamentals/intersection_slots.md similarity index 100% rename from docs/analyze/intersection_slots.md rename to docs/fundamentals/intersection_slots.md diff --git a/docs/analyze/pipelines.md b/docs/fundamentals/pipelines.md similarity index 100% rename from docs/analyze/pipelines.md rename to docs/fundamentals/pipelines.md diff --git a/docs/analyze/voronoi_slots.md b/docs/fundamentals/voronoi_slots.md similarity index 100% rename from docs/analyze/voronoi_slots.md rename to docs/fundamentals/voronoi_slots.md diff --git a/index.md b/index.md index 1e6ea47..af924e1 100644 --- a/index.md +++ b/index.md @@ -23,7 +23,7 @@ Use the [decision aid](decision-aid) to get a feeling if ImageC meets your requi docs/intro/index docs/starting/index -docs/analyze/index +docs/fundamentals/index docs/advanced/index :::