spacr 0.1.81__py3-none-any.whl → 0.2.0__py3-none-any.whl

spacr/resources/icons/abort.svg

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spacr/resources/icons/annotate.svg

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spacr/resources/icons/classify.svg

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spacr/resources/icons/download.svg

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spacr/resources/icons/make_masks.svg

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spacr/resources/icons/map_barcodes.svg

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spacr/resources/icons/mask.svg

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spacr/resources/icons/measure.svg

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spacr/resources/icons/run.svg

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spacr/resources/icons/run_2.svg

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spacr/resources/icons/sequencing.svg

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spacr/resources/icons/settings.svg

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spacr/resources/icons/train_cellpose.svg

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spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv

@@ -0,0 +1,23 @@
+Key,Value
+img_src,/nas_mnt/carruthers/patrick/Plaque_assay_training/train
+model_name,toxo_plaque
+model_type,cyto
+Signal_to_noise,10
+background,200
+remove_background,False
+learning_rate,0.2
+weight_decay,1e-05
+batch_size,8
+n_epochs,25000
+from_scratch,False
+diameter,30
+resize,True
+width_height,"[1120, 1120]"
+verbose,True
+channels,"[0, 0]"
+normalize,True
+percentiles,
+circular,False
+invert,False
+grayscale,True
+test,False

spacr/settings.py

@@ -1114,29 +1114,29 @@ categories = {
 }
 
 descriptions = {
-    'mask': "Generate Cellpose masks for Cells, Nuclei, and Pathogens. This module uses: preprocess_generate_masks from spacr.core.\n\nKey Features:\n- Automated Mask Generation: Automatically generate accurate masks for various cellular components using Cellpose, a robust deep learning model for cell segmentation.\n- Versatility: Capable of handling different types of biological samples, including cells, nuclei, and pathogens.\n- Integration: Directly integrates with other modules, providing the foundational masks required for subsequent analysis.",
+    'mask': "Generate Cellpose masks for Cells, Nuclei, and Pathogens. Function: preprocess_generate_masks from spacr.core.\n\nKey Features:\n- Automated Mask Generation: Automatically generate accurate masks for various cellular components using Cellpose, a robust deep learning model for cell segmentation.\n- Versatility: Capable of handling different types of biological samples, including cells, nuclei, and pathogens.\n- Integration: Directly integrates with other modules, providing the foundational masks required for subsequent analysis.",
     
-    'measure': "Capture Measurements from Cells, Nuclei, Pathogens, and Cytoplasm objects. Generate single object PNG images for one or several objects. (Requires masks from the Mask module). This module uses: measure_crop from spacr.measure.\n\nKey Features:\n- Comprehensive Measurement Capture: Obtain detailed measurements for various cellular components, including area, perimeter, intensity, and more.\n- Image Generation: Create high-resolution PNG images of individual objects, facilitating further analysis and visualization.\n- Mask Dependency: Requires accurate masks generated by the Mask module to ensure precise measurements.",
+    'measure': "Capture Measurements from Cells, Nuclei, Pathogens, and Cytoplasm objects. Generate single object PNG images for one or several objects. (Requires masks from the Mask module). Function: measure_crop from spacr.measure.\n\nKey Features:\n- Comprehensive Measurement Capture: Obtain detailed measurements for various cellular components, including area, perimeter, intensity, and more.\n- Image Generation: Create high-resolution PNG images of individual objects, facilitating further analysis and visualization.\n- Mask Dependency: Requires accurate masks generated by the Mask module to ensure precise measurements.",
     
-    'classify': "Train and Test any Torch Computer vision model. (Requires PNG images from the Measure module). This module uses: train_test_model from spacr.deep_spacr.\n\nKey Features:\n- Deep Learning Integration: Train and evaluate state-of-the-art Torch models for various classification tasks.\n- Flexible Training: Supports a wide range of Torch models, allowing customization based on specific research needs.\n- Data Requirement: Requires PNG images generated by the Measure module for training and testing.",
+    'classify': "Train and Test any Torch Computer vision model. (Requires PNG images from the Measure module). Function: train_test_model from spacr.deep_spacr.\n\nKey Features:\n- Deep Learning Integration: Train and evaluate state-of-the-art Torch models for various classification tasks.\n- Flexible Training: Supports a wide range of Torch models, allowing customization based on specific research needs.\n- Data Requirement: Requires PNG images generated by the Measure module for training and testing.",
     
-    'sequencing': "Find Barcodes and gRNA sequences in FASTQ files. (Requires paired-end FASTQ files, R1 and R2). This module uses: analyze_reads from spacr.sequencing.\n\nKey Features:\n- Barcode and gRNA Identification: Efficiently detect and extract barcode and gRNA sequences from raw sequencing data.\n- Paired-End Support: Specifically designed to handle paired-end FASTQ files, ensuring accurate sequence alignment and analysis.\n- High Throughput: Capable of processing large sequencing datasets quickly and accurately.",
+    'sequencing': "Find Barcodes and gRNA sequences in FASTQ files. (Requires paired-end FASTQ files, R1 and R2). Function: analyze_reads from spacr.sequencing.\n\nKey Features:\n- Barcode and gRNA Identification: Efficiently detect and extract barcode and gRNA sequences from raw sequencing data.\n- Paired-End Support: Specifically designed to handle paired-end FASTQ files, ensuring accurate sequence alignment and analysis.\n- High Throughput: Capable of processing large sequencing datasets quickly and accurately.",
     
-    'umap': "Generate UMAP or tSNE embeddings and represent points as single cell images. (Requires measurements.db and PNG images from the Measure module). This module uses: generate_image_umap from spacr.core.\n\nKey Features:\n- Dimensionality Reduction: Employ UMAP or tSNE algorithms to reduce high-dimensional data into two dimensions for visualization.\n- Single Cell Representation: Visualize embedding points as single cell images, providing an intuitive understanding of data clusters.\n- Data Integration: Requires measurements and images generated by the Measure module, ensuring comprehensive data representation.",
+    'umap': "Generate UMAP or tSNE embeddings and represent points as single cell images. (Requires measurements.db and PNG images from the Measure module). Function: generate_image_umap from spacr.core.\n\nKey Features:\n- Dimensionality Reduction: Employ UMAP or tSNE algorithms to reduce high-dimensional data into two dimensions for visualization.\n- Single Cell Representation: Visualize embedding points as single cell images, providing an intuitive understanding of data clusters.\n- Data Integration: Requires measurements and images generated by the Measure module, ensuring comprehensive data representation.",
     
-    'train_cellpose': "Train custom Cellpose models for your specific dataset. This module uses: train_cellpose_model from spacr.core.\n\nKey Features:\n- Custom Model Training: Train Cellpose models on your dataset to improve segmentation accuracy.\n- Data Adaptation: Tailor the model to handle specific types of biological samples more effectively.\n- Advanced Training Options: Supports various training parameters and configurations for optimized performance.",
+    'train_cellpose': "Train custom Cellpose models for your specific dataset. Function: train_cellpose_model from spacr.core.\n\nKey Features:\n- Custom Model Training: Train Cellpose models on your dataset to improve segmentation accuracy.\n- Data Adaptation: Tailor the model to handle specific types of biological samples more effectively.\n- Advanced Training Options: Supports various training parameters and configurations for optimized performance.",
     
-    'ml_analyze': "Perform machine learning analysis on your data. This module uses: ml_analysis_tools from spacr.ml.\n\nKey Features:\n- Comprehensive Analysis: Utilize a suite of machine learning tools for data analysis.\n- Customizable Workflows: Configure and run different ML algorithms based on your research requirements.\n- Integration: Works seamlessly with other modules to analyze data produced from various steps.",
+    'ml_analyze': "Perform machine learning analysis on your data. Function: ml_analysis_tools from spacr.ml.\n\nKey Features:\n- Comprehensive Analysis: Utilize a suite of machine learning tools for data analysis.\n- Customizable Workflows: Configure and run different ML algorithms based on your research requirements.\n- Integration: Works seamlessly with other modules to analyze data produced from various steps.",
     
-    'cellpose_masks': "Generate masks using Cellpose for all images in your dataset. This module uses: generate_masks from spacr.cellpose.\n\nKey Features:\n- Batch Processing: Generate masks for large sets of images efficiently.\n- Robust Segmentation: Leverage Cellpose's capabilities for accurate segmentation across diverse samples.\n- Automation: Automate the mask generation process for streamlined workflows.",
+    'cellpose_masks': "Generate masks using Cellpose for all images in your dataset. Function: generate_masks from spacr.cellpose.\n\nKey Features:\n- Batch Processing: Generate masks for large sets of images efficiently.\n- Robust Segmentation: Leverage Cellpose's capabilities for accurate segmentation across diverse samples.\n- Automation: Automate the mask generation process for streamlined workflows.",
     
-    'cellpose_all': "Run Cellpose on all images in your dataset and obtain masks and measurements. This module uses: cellpose_analysis from spacr.cellpose.\n\nKey Features:\n- End-to-End Analysis: Perform both segmentation and measurement extraction in a single step.\n- Efficiency: Process entire datasets with minimal manual intervention.\n- Comprehensive Output: Obtain detailed masks and corresponding measurements for further analysis.",
+    'cellpose_all': "Run Cellpose on all images in your dataset and obtain masks and measurements. Function: cellpose_analysis from spacr.cellpose.\n\nKey Features:\n- End-to-End Analysis: Perform both segmentation and measurement extraction in a single step.\n- Efficiency: Process entire datasets with minimal manual intervention.\n- Comprehensive Output: Obtain detailed masks and corresponding measurements for further analysis.",
     
-    'map_barcodes': "Map barcodes to your data for identification and tracking. This module uses: barcode_mapping_tools from spacr.sequencing.\n\nKey Features:\n- Barcode Integration: Efficiently map and integrate barcode information into your dataset.\n- Tracking: Enable tracking and identification of samples using barcodes.\n- Compatibility: Works with sequencing data to ensure accurate mapping and analysis.",
+    'map_barcodes': "Map barcodes to your data for identification and tracking. Function: barcode_mapping_tools from spacr.sequencing.\n\nKey Features:\n- Barcode Integration: Efficiently map and integrate barcode information into your dataset.\n- Tracking: Enable tracking and identification of samples using barcodes.\n- Compatibility: Works with sequencing data to ensure accurate mapping and analysis.",
     
-    'regression': "Perform regression analysis on your data. This module uses: regression_tools from spacr.analysis.\n\nKey Features:\n- Statistical Analysis: Conduct various types of regression analysis to identify relationships within your data.\n- Flexible Options: Supports multiple regression models and configurations.\n- Data Insight: Gain deeper insights into your dataset through advanced regression techniques.",
+    'regression': "Perform regression analysis on your data. Function: regression_tools from spacr.analysis.\n\nKey Features:\n- Statistical Analysis: Conduct various types of regression analysis to identify relationships within your data.\n- Flexible Options: Supports multiple regression models and configurations.\n- Data Insight: Gain deeper insights into your dataset through advanced regression techniques.",
     
-    'recruitment': "Analyze recruitment data to understand sample recruitment dynamics. This module uses: recruitment_analysis_tools from spacr.analysis.\n\nKey Features:\n- Recruitment Analysis: Investigate and analyze the recruitment of samples over time or conditions.\n- Visualization: Generate visualizations to represent recruitment trends and patterns.\n- Integration: Utilize data from various sources for a comprehensive recruitment analysis."
+    'recruitment': "Analyze recruitment data to understand sample recruitment dynamics. Function: recruitment_analysis_tools from spacr.analysis.\n\nKey Features:\n- Recruitment Analysis: Investigate and analyze the recruitment of samples over time or conditions.\n- Visualization: Generate visualizations to represent recruitment trends and patterns.\n- Integration: Utilize data from various sources for a comprehensive recruitment analysis."
 }
 
 def set_annotate_default_settings(settings):

{spacr-0.1.81.dist-info → spacr-0.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.81
+Version: 0.2.0
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

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