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plant-seg-tools

Simple python tools for plant-seg https://github.com/hci-unihd/plant-seg

Index

Install PlantSeg Tools

conda activate plant-seg
  • clone this repository locally on our machine, in the terminal navigate to the desired install location and execute:
git clone https://github.com/hci-unihd/plant-seg-tools.git
  • install plant-seg-tools:
cd plant-seg-tools
pip install .

Additional dependencies

While having your conda environment activated:

  • In oder to use seg2mesh
conda install -c conda-forge ray vtk
  • In order to use the trimesh backend of plantsegtools/meshes, you will need to install trimesh using:
conda install -c conda-forge trimesh
  • In order to use the training configurator wizard you need to install PyInquirer
pip install PyInquirer

Install proofreading tool

  • create a new conda environment (at the moment plant-seg and the proofreading tools are not compatible). On a fresh terminal execute:
conda create -n plant-seg-proofreading -c conda-forge python numpy numba scipy matplotlib scikit-image pyaml h5py tqdm napari pyqt=5.12.3
conda activate plant-seg-proofreading
  • clone this repository locally on our machine, in the terminal navigate to the desired install location and execute:
git clone https://github.com/hci-unihd/plant-seg-tools.git
  • install plant-seg-tools:
cd plant-seg-tools
pip install .

Segmentation to Meshes

Basic usage

From the project root (plant-seg-tools) run the seg2mesh script using:

python useful-scripts/seg2mesh.py --path 'PATHTOSEGMENTATIONSTACK'

Optional arguments guide

  • --new-base: optional custom saving directory. If not given the ply will be saved in the same dir as the source.
  • --h5-dataset: h5 internal dataset name. Default: segmentation.
  • --labels: List of labels to process. By default, the script will process all labels.
  • --step-size: Step size for the marching cube algorithm, larger steps yield a coarser but faster result. Default 2.
  • --crop: Crop the dataset, takes as input a bounding box. eg --crop 10, 0, 0 15, -1, -1.
  • --voxel-size: Voxel size [Z, Y, X] of the segmentation stack. By default, voxel size is read from the source file, if this is not possible voxel-size is set to [1, 1, 1].
  • --min-size: Minimum cell size. Default 50.
  • --max-size: Maximum cell size. Default inf.
  • --relabel: If this argument is passed the pipeline will relabel the segmentation. This will ensure the contiguity of each segment but will change the labels.
  • --check-cc: If this argument is passed the pipeline will check if each label is has a single connected component (cc). If multiple cc are present only the largest will be processed.
  • --ignore-labels: List of labels to ignore. By default, only background (label 0) is ignored.
  • --reduction: If reduction > 0 a decimation filter is applied.MaxValue: 1.0 (100%reduction).
  • --smoothing: To apply a Laplacian smoothing filter.
  • --use-ray: If you use ray flag is used the multiprocessing flag is managed by ray.
  • --multiprocessing: Define the number of cores to use for parallel processing. Default value (-1) will try to parallelize over all available processors.

Proofreading tool

Basic usage

From the project root (plant-seg-tools) run the proofreading tool using:

  • if the stack is coming from PlantSeg
python useful-scripts/proofreading.py --path-raw 'PATHTORAWSTACK' --path-seg 'PATHTOSEGMENTATIONSTACK' --dataset-seg segmentation

or in short

python useful-scripts/proofreading.py --r 'PATHTORAWSTACK' -s 'PATHTOSEGMENTATIONSTACK' -ds segmentation
  • if you want to continue working on a stack exported with the proofreading tool (or if segmentation and raw images are together in the same h5 file):
python useful-scripts/proofreading.py -r 'PATHTORAWSTACK (convetional name *_proofreading.h5')'

add to bashrc

alias  proofreading="[user-dir-location]/miniconda3/envs/plant-seg-proofreading/bin/python [plant-seg-tools-location]/plant-seg-tools/useful-scripts/proofreading.py"

Keybinding Guide:

  • s: Save stack
  • n: Merge or split from seeds
  • ctrl+n: Undo merge or split from seeds
  • c: Clean seeds
  • o: Mark/un-mark correct segmentation
  • b: show/un-show correct segmentation layer
  • j: Update boundaries from segmentation
  • k: Update segmentation from boundaries

Navigation

  • ctrl + arrows: to move the field of view
  • alt + down/up arrows: to increase or decrease the field of view

Optional arguments guide

  • -dr or --dataset-raw: name of the dataset containing the raw boundary image. Only used if raw boundary image is in h5 format. default raw.
  • -ds or --dataset-seg: name of the dataset containing the cell segmentation. Only used if segmentation is in h5 format. default label.
  • -xy or --xy-size: field of view size along the xy-plane. Larger field of view might slow down the tool.
  • -z or --z-size: field of view size along z. Only for 3D. Larger field of view might slow down the tool.

Automated Segmentation Proofread from seeds

Basic usage

python useful-scripts/fix_over_under_from_nuclei.py --seg-path 'PATHTOSEGMENTATIONSTACK' --nuclei-seg-path 'PATHTONUCLEISEGMENTATIONSTACK' 

Optional arguments guide

  • --t-merge: Overlap merging threshold, between 0-1.
  • --t-split: Overlap split threshold, between 0-1.
  • --quantiles: Nuclei size below and above the defined quantiles will be ignored.
  • --scaling: Scaling factor for the segmentation.
  • --export-h5: In order to export the segmentation as h5.
  • --boundaries-path: path to boundaries predictions file.

Evaluation

Basic usage

python useful-scripts/evaluation_segmentation.py -s PATHTOSEG -g PATHTOGT 

Optional arguments guide

  • -ds or --dataset-seg: if h5 contains dataset name to segmentation
    • -dg or --dataset-gt: if h5 contains dataset name to ground-truth

plantsegtools's People

Contributors

lorenzocerrone avatar alexismaizel avatar

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