From 9d96d511b1df3a4d9c291e78f9269469720fe5b1 Mon Sep 17 00:00:00 2001 From: kapoorlab Date: Sun, 3 Sep 2023 15:20:51 +0200 Subject: [PATCH] update readme --- README.md | 14 ++++---- _build/.doctrees/README.doctree | Bin 56802 -> 51627 bytes _build/.doctrees/environment.pickle | Bin 33397 -> 33464 bytes _build/html/README.html | 50 ++++++++++++++-------------- _build/html/_sources/README.md | 14 ++++---- 5 files changed, 39 insertions(+), 39 deletions(-) diff --git a/README.md b/README.md index 1f3969f..0bdb8e3 100644 --- a/README.md +++ b/README.md @@ -30,19 +30,19 @@ VollSeg comes with different options to combine CARE based denoising with UNET, | Example Image | Description | Training Data | Trained Model | GT image | Optimal combination | Notebook Code | Model Prediction | Metrics | | --- | --- |--- | --- |--- | --- |--- | --- | --- | -| | Light sheet fused from four angles 3D single channel| [Training Data ~320 GB](https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5)| [UNET model](https://zenodo.org/record/6337699) | | UNET model, slice_merge = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Ascadian_Embryo.ipynb) | | | +| | Light sheet fused from four angles 3D single channel| [Training Data ~320 GB](https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5)| [UNET model](https://zenodo.org/record/6337699) | | UNET model, slice_merge = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Ascadian_Embryo.ipynb) | | | | | | | | | | | | | -| | Confocal microscopy 3D single channel 8 bit| [Training Data](https://zenodo.org/record/5904082#.Yi8-BnrMJD8)| [Denoising Model](https://zenodo.org/record/5910645/) and [StarDist Model](https://zenodo.org/record/6354077/) | | StarDist model + Denoising Model, dounet = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Mamary_gland.ipynb) | | | +| | Confocal microscopy 3D single channel 8 bit| [Training Data](https://zenodo.org/record/5904082#.Yi8-BnrMJD8)| [Denoising Model](https://zenodo.org/record/5910645/) and [StarDist Model](https://zenodo.org/record/6354077/) | | StarDist model + Denoising Model, dounet = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Mamary_gland.ipynb) | | | | | | | | | | | | | -| | LaserScanningConfocalMicroscopy 2D single channel| [Dataset](https://zenodo.org/record/6076614#.YjBaNnrMJD8)| [UNET Model](https://zenodo.org/record/6060378/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_tissue_segmentation.ipynb) | | No Metrics | +| | LaserScanningConfocalMicroscopy 2D single channel| [Dataset](https://zenodo.org/record/6076614#.YjBaNnrMJD8)| [UNET Model](https://zenodo.org/record/6060378/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_tissue_segmentation.ipynb) | | No Metrics | | | | | | | | | | | -| | TIRF + MultiKymograph Fiji tool 2D single channel| [Training Dataset](https://zenodo.org/record/6355705/files/Microtubule_edgedetector_training.zip)| [UNET Model](https://zenodo.org/record/6355705/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | No Metrics | +| | TIRF + MultiKymograph Fiji tool 2D single channel| [Training Dataset](https://zenodo.org/record/6355705/files/Microtubule_edgedetector_training.zip)| [UNET Model](https://zenodo.org/record/6355705/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | No Metrics | | | | | | | | | | | -| | XRay of Lung 2D single channel| [Training Dataset](https://www.kaggle.com/nikhilpandey360/lung-segmentation-from-chest-x-ray-dataset)| [UNET Model](https://zenodo.org/record/6060177/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | | +| | XRay of Lung 2D single channel| [Training Dataset](https://www.kaggle.com/nikhilpandey360/lung-segmentation-from-chest-x-ray-dataset)| [UNET Model](https://zenodo.org/record/6060177/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | | | | | | | | | | | | -| | LaserScanningConfocalMicroscopy 2D single channell| [Test Dataset](https://zenodo.org/record/6359349/)|Private | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | No metrics | +| | LaserScanningConfocalMicroscopy 2D single channell| [Test Dataset](https://zenodo.org/record/6359349/)|Private | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | No metrics | | | | | | | | | | | -| | LaserScanningConfocalMicroscopy 3D single channell| [Test Dataset](https://zenodo.org/record/6359295/)|Private | | UNET model + StarDist model + ROI model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_star_roi.ipynb) | | | +| | LaserScanningConfocalMicroscopy 3D single channell| [Test Dataset](https://zenodo.org/record/6359295/)|Private | | UNET model + StarDist model + ROI model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_star_roi.ipynb) | | | ## Troubleshooting & Support diff --git a/_build/.doctrees/README.doctree b/_build/.doctrees/README.doctree index 8699af3987bb81cddaf8ca94d6a0ae421b589926..e186eacf6bc1a8e0144d3248ea29ba0f9d74320e 100644 GIT binary patch delta 1552 zcmZvcF=$gk7{`&9_c9zgN~FOtI*3EXRx~!gBz;X|+Lxv_51S?pD3wrb2h(DQMl7}+ zG6)idBOpq^L9(Pn>rL9BbqP@jZcc(Af*FbkE?oq@o9_GG8^0g_-`#z@fAal6YcoyX z)*G)s?(5Gkk!)<`{=M+}gL3>Fs}E1Hq2VB688lBYt3~<4kpY9)iu`Ca#hyQ=h)tr| zlJa7-tC2ZHuEuYpd6q7Rp2Em9+pAF)9_xc>(SmBxa;Zg2s&A9)2ANcDJ+Tw)C>M0G zfvR6+{KSqMB&CS8+zgt>#B*W9l&k)AerP1GxFhp-(3}%4jAZ4iUkiN@T`FbS;zH2H z))Ib|@ugDFAdYgUwH#tE?xs9gMBMF;UY2h^TmI}LH^DgtG~2?5ksH$eveMGX0&qjj zT)i$A@Zw?##JRb;<0mEMki(6I@Jq0DFFElYi~v5C->swvm?&iTfa0? zMu${tNx6m>7i%ESE43$}P;9gAE}mexc$@Wk9Td%JnDY5*(*zTu!no7;qmfzV*|C=y z7OqglX3(6LwY&JL4|t&Ib^}f52AXO9ySZbKY30%nZ|2aP7IlGhd#i&Ll%d{vqL8{%tQI!XRA8o2&t>Zk5HF`-BiZO_a7x3#1Vw* 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Examples

+

Light sheet fused from four angles 3D single channel

Training Data ~320 GB

UNET model

-

+

UNET model, slice_merge = False

Colab Notebook

-

-

+

+

@@ -420,15 +420,15 @@

Examples

+

Confocal microscopy 3D single channel 8 bit

Training Data

Denoising Model and StarDist Model

-

+

StarDist model + Denoising Model, dounet = False

Colab Notebook

-

-

+

+

@@ -440,14 +440,14 @@

Examples

+

LaserScanningConfocalMicroscopy 2D single channel

Dataset

UNET Model

-

+

UNET model

Colab Notebook

-

+

No Metrics

@@ -460,14 +460,14 @@

Examples

+

TIRF + MultiKymograph Fiji tool 2D single channel

Training Dataset

UNET Model

-

+

UNET model

Colab Notebook

-

+

No Metrics

@@ -480,15 +480,15 @@

Examples

+

XRay of Lung 2D single channel

Training Dataset

UNET Model

-

+

UNET model

Colab Notebook

-

-

+

+

@@ -500,14 +500,14 @@

Examples

+

LaserScanningConfocalMicroscopy 2D single channell

Test Dataset

Private

-

+

UNET model

Colab Notebook

-

+

No metrics

@@ -520,15 +520,15 @@

Examples

+

LaserScanningConfocalMicroscopy 3D single channell

Test Dataset

Private

-

+

UNET model + StarDist model + ROI model

Colab Notebook

-

-

+

+

diff --git a/_build/html/_sources/README.md b/_build/html/_sources/README.md index 1f3969f..0bdb8e3 100644 --- a/_build/html/_sources/README.md +++ b/_build/html/_sources/README.md @@ -30,19 +30,19 @@ VollSeg comes with different options to combine CARE based denoising with UNET, | Example Image | Description | Training Data | Trained Model | GT image | Optimal combination | Notebook Code | Model Prediction | Metrics | | --- | --- |--- | --- |--- | --- |--- | --- | --- | -| | Light sheet fused from four angles 3D single channel| [Training Data ~320 GB](https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5)| [UNET model](https://zenodo.org/record/6337699) | | UNET model, slice_merge = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Ascadian_Embryo.ipynb) | | | +| | Light sheet fused from four angles 3D single channel| [Training Data ~320 GB](https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5)| [UNET model](https://zenodo.org/record/6337699) | | UNET model, slice_merge = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Ascadian_Embryo.ipynb) | | | | | | | | | | | | | -| | Confocal microscopy 3D single channel 8 bit| [Training Data](https://zenodo.org/record/5904082#.Yi8-BnrMJD8)| [Denoising Model](https://zenodo.org/record/5910645/) and [StarDist Model](https://zenodo.org/record/6354077/) | | StarDist model + Denoising Model, dounet = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Mamary_gland.ipynb) | | | +| | Confocal microscopy 3D single channel 8 bit| [Training Data](https://zenodo.org/record/5904082#.Yi8-BnrMJD8)| [Denoising Model](https://zenodo.org/record/5910645/) and [StarDist Model](https://zenodo.org/record/6354077/) | | StarDist model + Denoising Model, dounet = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Mamary_gland.ipynb) | | | | | | | | | | | | | -| | LaserScanningConfocalMicroscopy 2D single channel| [Dataset](https://zenodo.org/record/6076614#.YjBaNnrMJD8)| [UNET Model](https://zenodo.org/record/6060378/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_tissue_segmentation.ipynb) | | No Metrics | +| | LaserScanningConfocalMicroscopy 2D single channel| [Dataset](https://zenodo.org/record/6076614#.YjBaNnrMJD8)| [UNET Model](https://zenodo.org/record/6060378/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_tissue_segmentation.ipynb) | | No Metrics | | | | | | | | | | | -| | TIRF + MultiKymograph Fiji tool 2D single channel| [Training Dataset](https://zenodo.org/record/6355705/files/Microtubule_edgedetector_training.zip)| [UNET Model](https://zenodo.org/record/6355705/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | No Metrics | +| | TIRF + MultiKymograph Fiji tool 2D single channel| [Training Dataset](https://zenodo.org/record/6355705/files/Microtubule_edgedetector_training.zip)| [UNET Model](https://zenodo.org/record/6355705/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | No Metrics | | | | | | | | | | | -| | XRay of Lung 2D single channel| [Training Dataset](https://www.kaggle.com/nikhilpandey360/lung-segmentation-from-chest-x-ray-dataset)| [UNET Model](https://zenodo.org/record/6060177/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | | +| | XRay of Lung 2D single channel| [Training Dataset](https://www.kaggle.com/nikhilpandey360/lung-segmentation-from-chest-x-ray-dataset)| [UNET Model](https://zenodo.org/record/6060177/) | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | | | | | | | | | | | | -| | LaserScanningConfocalMicroscopy 2D single channell| [Test Dataset](https://zenodo.org/record/6359349/)|Private | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | No metrics | +| | LaserScanningConfocalMicroscopy 2D single channell| [Test Dataset](https://zenodo.org/record/6359349/)|Private | | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) | | No metrics | | | | | | | | | | | -| | LaserScanningConfocalMicroscopy 3D single channell| [Test Dataset](https://zenodo.org/record/6359295/)|Private | | UNET model + StarDist model + ROI model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_star_roi.ipynb) | | | +| | LaserScanningConfocalMicroscopy 3D single channell| [Test Dataset](https://zenodo.org/record/6359295/)|Private | | UNET model + StarDist model + ROI model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_star_roi.ipynb) | | | ## Troubleshooting & Support