deepliif 1.1.6__py3-none-any.whl → 1.1.7__py3-none-any.whl

deepliif/models/__init__.py

@@ -323,7 +323,7 @@ def inference(img, tile_size, overlap_size, model_path, use_torchserve=False, ea
     for i in range(cols):
         for j in range(rows):
             tile = extract_tile(rescaled, tile_size, overlap_size, i, j)
-            res = run_fn(tile, model_path, eager_mode)
+            res = run_wrapper(tile, run_fn, model_path, eager_mode)
 
             stitch_tile(images['Hema'], res['G1'], tile_size, overlap_size, i, j)
             stitch_tile(images['DAPI'], res['G2'], tile_size, overlap_size, i, j)

{deepliif-1.1.6.dist-info → deepliif-1.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.1.6
+Version: 1.1.7
 Summary: DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification
 Home-page: https://github.com/nadeemlab/DeepLIIF
 Author: Parmida93
@@ -26,20 +26,16 @@ 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 Link</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 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 Link</a>
+    <a href="https://arxiv.org/abs/2305.16465">MICCAI'23 link</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>
@@ -366,6 +362,9 @@ 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 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 +378,7 @@ 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 +399,10 @@ 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}
+}
 ```

{deepliif-1.1.6.dist-info → deepliif-1.1.7.dist-info}/RECORD

@@ -11,7 +11,7 @@ deepliif/data/single_dataset.py,sha256=hWjqTkRESEMppZj_r8bi3G0hAZ5EfvXYgE_qRbpiE
 deepliif/data/template_dataset.py,sha256=PCDBnFRzRKReaeWgKUZmW0LrzRByI9adrKDJ6SN2KMs,3592
 deepliif/data/unaligned_dataset.py,sha256=m7j-CX-hkXbhg96NSEcaCagNVhTuXKkMsBADdMEJDBA,3393
 deepliif/models/DeepLIIF_model.py,sha256=CE-fs9g9zaeUtBKGEYtEsVVMRRQ8V-i9cOWO7cy4Z0U,20669
-deepliif/models/__init__.py,sha256=4L842F6d6T2ULPalv_aJgZhu5rMgZvb5Sa4cNz3IKm4,17765
+deepliif/models/__init__.py,sha256=FRjj-kFG67MG6VAdsbehJkloi2GDO9vTbZoktPkVykc,17778
 deepliif/models/base_model.py,sha256=MGIsgMbhbfJyKMW_IiM4TCxvvHSioqKjdbti1k9u4ko,12951
 deepliif/models/networks.py,sha256=bN4yjRdE413efUESq8pvhzPDgFCTwFKXyQOrRqHckWY,32177
 deepliif/options/__init__.py,sha256=WEkvROZkYWDVDCrB_P66wPYYU2cMgBmVx2i7_BpEKq0,137
@@ -25,9 +25,9 @@ deepliif/util/html.py,sha256=RNAONZ4opP-bViahgmpSbHwOc6jXKQRnWRAVIaeIvac,3309
 deepliif/util/image_pool.py,sha256=M89Hc7DblRWroNP71S9mAdRn7h3DrhPFPjqFxxZYSgw,2280
 deepliif/util/util.py,sha256=bTArzuhIMGgGweH0v5rkiHrqBxc24BDv12rssOE9OoI,4636
 deepliif/util/visualizer.py,sha256=5V1lWidHqssJX21jn1P5-bOVgtrEXKVaQgnMWAsMfqg,15636
-deepliif-1.1.6.dist-info/LICENSE.md,sha256=HlZw_UPS6EtJimJ_Ci7xKh-S5Iubs0Z8y8E6EZ3ZNyE,956
-deepliif-1.1.6.dist-info/METADATA,sha256=6eDCIj2ragujJw-K_PpMBKcoppZbH5BHw7q_GVsJSL8,23363
-deepliif-1.1.6.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-deepliif-1.1.6.dist-info/entry_points.txt,sha256=f70-10j2q68o_rDlsE3hspnv4ejlDnXwwGZ9JJ-3yF4,37
-deepliif-1.1.6.dist-info/top_level.txt,sha256=vLDK5YKmDz08E7PywuvEjAo7dM5rnIpsjR4c0ubQCnc,13
-deepliif-1.1.6.dist-info/RECORD,,
+deepliif-1.1.7.dist-info/LICENSE.md,sha256=HlZw_UPS6EtJimJ_Ci7xKh-S5Iubs0Z8y8E6EZ3ZNyE,956
+deepliif-1.1.7.dist-info/METADATA,sha256=cTL4yv1e45pY0Isz-4qFPE8QYLS-9ffQTBwbB6aaLsI,24145
+deepliif-1.1.7.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+deepliif-1.1.7.dist-info/entry_points.txt,sha256=f70-10j2q68o_rDlsE3hspnv4ejlDnXwwGZ9JJ-3yF4,37
+deepliif-1.1.7.dist-info/top_level.txt,sha256=vLDK5YKmDz08E7PywuvEjAo7dM5rnIpsjR4c0ubQCnc,13
+deepliif-1.1.7.dist-info/RECORD,,