deepliif 1.1.6__py3-none-any.whl → 1.1.8__py3-none-any.whl

{deepliif-1.1.6.dist-info → deepliif-1.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.1.6
+Version: 1.1.8
 Summary: DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification
 Home-page: https://github.com/nadeemlab/DeepLIIF
 Author: Parmida93
@@ -26,20 +26,18 @@ Requires-Dist: python-bioformats (>=4.0.6)
     <img src="./images/DeepLIIF_logo.png" width="50%">
     <h3 align="center"><strong>Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification</strong></h3>
     <p align="center">
-    <a href="https://doi.org/10.1101/2021.05.01.442219">Journal Preprint</a>
+    <a href="https://rdcu.be/cKSBz">Nature MI'22</a>
     |
-    <a href="https://rdcu.be/cKSBz">Journal Link</a>
+    <a href="https://openaccess.thecvf.com/content/CVPR2022/html/Ghahremani_DeepLIIF_An_Online_Platform_for_Quantification_of_Clinical_Pathology_Slides_CVPR_2022_paper.html">CVPR'22</a>
     |
-    <a href="https://openaccess.thecvf.com/content/CVPR2022/html/Ghahremani_DeepLIIF_An_Online_Platform_for_Quantification_of_Clinical_Pathology_Slides_CVPR_2022_paper.html">CVPR Link</a>
+    <a href="https://arxiv.org/abs/2305.16465">MICCAI'23</a>
+    |
+    <a href="https://onlinelibrary.wiley.com/share/author/4AEBAGEHSZE9GDP3H8MN?target=10.1111/his.15048">Histopathology'23</a>
     |
     <a href="https://deepliif.org/">Cloud Deployment</a>
     |
     <a href="https://nadeemlab.github.io/DeepLIIF/">Documentation</a>
     |
-    <a href="#docker">Docker</a>
-    |
-    <a href="https://github.com/nadeemlab/DeepLIIF/tree/main/ImageJ_Plugin">ImageJ Plugin</a>
-    |
     <a href="#support">Support</a>
   </p>
 </p>
@@ -231,8 +229,7 @@ on how to deploy the model with Torchserve and for an example of how to run the
 We provide a Dockerfile that can be used to run the DeepLIIF models inside a container.
 First, you need to install the [Docker Engine](https://docs.docker.com/engine/install/ubuntu/).
 After installing the Docker, you need to follow these steps:
-* Download the pretrained model and place them in DeepLIIF/checkpoints/DeepLIIF_Latest_Model.
-* Change XXX of the **WORKDIR** line in the **DockerFile** to the directory containing the DeepLIIF project. 
+* Download the pretrained model [here](https://zenodo.org/record/4751737#.YKRTS0NKhH4) and place them in DeepLIIF/model-server/DeepLIIF_Latest_Model.
 * To create a docker image from the docker file:
 ```
 docker build -t cuda/deepliif .
@@ -241,7 +238,7 @@ The image is then used as a base. You can copy and use it to run an application.
 environment in which to run, referred to as a container.
 * To create and run a container:
 ```
- docker run -it -v `pwd`:`pwd` -w `pwd` cuda/deepliif deepliif test --input-dir Sample_Large_Tissues
+ docker run -it -v `pwd`:`pwd` -w `pwd` cuda/deepliif deepliif test --input-dir Sample_Large_Tissues --tile-size 512
 ```
 When you run a container from the image, the `deepliif` CLI will be available.
 You can easily run any CLI command in the activated environment and copy the results from the docker container to the host.
@@ -366,6 +363,9 @@ for the same slide (de novo staining) and would like to contribute that data for
 co-registration, whole-cell multiplex segmentation via [ImPartial](https://github.com/nadeemlab/ImPartial), train the 
 DeepLIIF model and release back to the community with full credit to the contributors.
 
+- [x] **Memorial Sloan Kettering Cancer Center** [AI-ready immunohistochemistry and multiplex immunofluorescence dataset](https://zenodo.org/record/4751737#.YKRTS0NKhH4) for breast, lung, and bladder cancers (**Nature Machine Intelligence'22**)
+- [x] **Moffitt Cancer Center** [AI-ready multiplex immunofluorescence and multiplex immunohistochemistry dataset](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=70226184) for head-and-neck squamous cell carcinoma (**MICCAI'23**)   
+
 ## Support
 Please use the [Image.sc Forum](https://forum.image.sc/tag/deepliif) for discussion and questions related to DeepLIIF.
 
@@ -379,7 +379,7 @@ and is available for non-commercial academic purposes.
 * This code is inspired by [CycleGAN and pix2pix in PyTorch](https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix).
 
 ## Reference
-If you find our work useful in your research or if you use parts of this code, please cite our paper:
+If you find our work useful in your research or if you use parts of this code or our released dataset, please cite the following papers:
 ```
 @article{ghahremani2022deep,
   title={Deep learning-inferred multiplex immunofluorescence for immunohistochemical image quantification},
@@ -400,4 +400,18 @@ If you find our work useful in your research or if you use parts of this code, p
   year={2022}
 }
 
+@article{ghahremani2023deepliifdataset,
+  title={An AI-Ready Multiplex Staining Dataset for Reproducible and Accurate Characterization of Tumor Immune Microenvironment},
+  author={Ghahremani, Parmida and Marino, Joseph and Hernandez-Prera, Juan and V. de la Iglesia, Janis and JC Slebos, Robbert and H. Chung, Christine and Nadeem, Saad},
+  journal={International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
+  year={2023}
+}
+
+@article{nadeem2023ki67validationMTC,
+  author = {Nadeem, Saad and Hanna, Matthew G and Viswanathan, Kartik and Marino, Joseph and Ahadi, Mahsa and Alzumaili, Bayan and Bani, Mohamed-Amine and Chiarucci, Federico and Chou, Angela and De Leo, Antonio and Fuchs, Talia L and Lubin, Daniel J and Luxford, Catherine and Magliocca, Kelly and Martinez, Germán and Shi, Qiuying and Sidhu, Stan and Al Ghuzlan, Abir and Gill, Anthony J and Tallini, Giovanni and Ghossein, Ronald and Xu, Bin},
+  title = {Ki67 proliferation index in medullary thyroid carcinoma: a comparative study of multiple counting methods and validation of image analysis and deep learning platforms},
+  journal = {Histopathology},
+  year = {2023},
+  doi = {https://doi.org/10.1111/his.15048}
+}
 ```

{deepliif-1.1.6.dist-info → deepliif-1.1.8.dist-info}/RECORD

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