deepliif 1.1.7__py3-none-any.whl → 1.1.9__py3-none-any.whl

{deepliif-1.1.7.dist-info → deepliif-1.1.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.1.7
+Version: 1.1.9
 Summary: DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification
 Home-page: https://github.com/nadeemlab/DeepLIIF
 Author: Parmida93
@@ -26,11 +26,13 @@ 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://rdcu.be/cKSBz">Nature MI'22 Link</a>
+    <a href="https://rdcu.be/cKSBz">Nature MI'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'22 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://arxiv.org/abs/2305.16465">MICCAI'23 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>
     |
@@ -227,8 +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 .
@@ -237,7 +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.
@@ -268,7 +269,7 @@ img (required)
 file: image to run the models on
 
 resolution
-string: resolution used to scan the slide (10x, 20x, 40x), defaults to 20x 
+string: resolution used to scan the slide (10x, 20x, 40x), defaults to 40x 
 
 pil
 boolean: if true, use PIL.Image.open() to load the image, instead of python-bioformats
@@ -297,9 +298,9 @@ res = requests.post(
     files={
         'img': open(f'{images_dir}/{filename}', 'rb')
     },
-    # optional param that can be 10x, 20x (default) or 40x
+    # optional param that can be 10x, 20x, or 40x (default)
     params={
-        'resolution': '20x'
+        'resolution': '40x'
     }
 )
 
@@ -363,7 +364,7 @@ co-registration, whole-cell multiplex segmentation via [ImPartial](https://githu
 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 for head-and-neck squamous cell carcinoma (**MICCAI'23**)   
+- [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.
@@ -405,4 +406,12 @@ If you find our work useful in your research or if you use parts of this code or
   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-1.1.7.dist-info → deepliif-1.1.9.dist-info}/RECORD

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