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| import gradio as gr | |
| from PIL import Image | |
| # Single image analysis function (your existing logic) | |
| def analyze_image(image, min_size, circularity, do_necrosis=True): | |
| import Organoid_Analyzer_AI2_HF as analyzer | |
| processed_img, picname, excelname = analyzer.main([image, min_size, circularity,do_necrosis]) | |
| return Image.fromarray(processed_img), picname, excelname | |
| # Z-stack analysis function (adapt with your own logic) | |
| def analyze_zstack(images, min_size, circularity, distance_cutoff=30, overlap_cutoff=0.4, do_necrosis=True): | |
| import Organoid_Analyzer_AI_zstack2_HF as analyzer | |
| images = [Image.open(f.name) for f in images] | |
| processed_img, picname, excelname = analyzer.main( | |
| [images, min_size, circularity, distance_cutoff, overlap_cutoff, do_necrosis] | |
| ) | |
| return Image.fromarray(processed_img), picname, excelname | |
| with gr.Blocks() as demo: | |
| gr.Markdown("# AI Organoid Analyzer\nUpload an image (or Z-Stack) to run organoid analysis.") | |
| z_stack_checkbox = gr.Checkbox(label="Enable Z-Stack", value=False) | |
| do_necrosis_checkbox = gr.Checkbox(label="Enable necrosis detection", value=False) | |
| image_input_single = gr.Image(type="pil", label="Upload Image", visible=True) | |
| image_input_multi = gr.File(file_count="multiple", type="filepath", label="Upload Z-Stack Images", visible=False) | |
| min_size_input = gr.Number(label="Minimum Organoid Size (pixels)", value=1000) | |
| circularity_input = gr.Number(label="Minimum Circularity", value=0.25) | |
| zstack_distance_cutoff_input = gr.Number(label="Z-Stack Centroid Distance Cutoff (pixels)", value=30, visible=False) | |
| zstack_overlap_cutoff_input = gr.Number(label="Z-Stack Colony Overlap Cutoff", value=0.4, visible=False) | |
| output_image = gr.Image(type="pil", label="Analyzed Image") | |
| output_file_img = gr.File(label="Download Image") | |
| output_file_excel = gr.File(label="Download results (Excel)") | |
| process_btn = gr.Button("Process") | |
| def toggle_inputs(z_stack_enabled): | |
| return ( | |
| gr.update(visible=not z_stack_enabled), # single input | |
| gr.update(visible=z_stack_enabled), # multi input | |
| gr.update(visible=z_stack_enabled), # zstack_distance_cutoff_input | |
| gr.update(visible=z_stack_enabled) # zstack_overlap_cutoff_input | |
| ) | |
| z_stack_checkbox.change( | |
| toggle_inputs, | |
| inputs=z_stack_checkbox, | |
| outputs=[ | |
| image_input_single, | |
| image_input_multi, | |
| zstack_distance_cutoff_input, | |
| zstack_overlap_cutoff_input]) | |
| def conditional_analyze(z_stack, single_image, multi_images, min_size, circularity, do_necrosis, distance_cutoff, overlap_cutoff): | |
| if z_stack: | |
| return analyze_zstack(multi_images, min_size, circularity, distance_cutoff, overlap_cutoff, do_necrosis) | |
| else: | |
| return analyze_image(single_image, min_size, circularity, do_necrosis) | |
| process_btn.click( | |
| conditional_analyze, | |
| inputs=[ | |
| z_stack_checkbox, | |
| image_input_single, | |
| image_input_multi, | |
| min_size_input, | |
| circularity_input, | |
| do_necrosis_checkbox, | |
| zstack_distance_cutoff_input, | |
| zstack_overlap_cutoff_input | |
| ], | |
| outputs=[output_image, output_file_img, output_file_excel]) | |
| demo.launch() | |