Accelerate data driven research on embryos with deep learning models :microscope:
pip install devolearn
from devolearn import cell_membrane_segmentor
segmentor = cell_membrane_segmentor()
seg_pred = segmentor.predict(image_path = "sample_data/images/seg_sample.jpg")
plt.imshow(seg_pred)
plt.show()
filenames = segmentor.predict_from_video(video_path = "sample_data/videos/seg_sample.mov", centroid_mode = False, save_folder = "preds")
seg_pred, centroids = segmentor.predict(image_path = "sample_data/images/seg_sample.jpg", centroid_mode = True)
plt.imshow(seg_pred)
plt.show()
df = segmentor.predict_from_video(video_path = "sample_data/videos/seg_sample.mov", centroid_mode = True, save_folder = "preds")
df.to_csv("centroids.csv")
from devolearn import cell_nucleus_segmentor
segmentor = cell_nucleus_segmentor()
seg_pred = segmentor.predict(image_path = "sample_data/images/nucleus_seg_sample.jpg")
plt.imshow(seg_pred)
plt.show()
from devolearn import Generator, embryo_generator_model
generator = embryo_generator_model()
gen_image = generator.generate()
plt.imshow(gen_image)
plt.show()
foldername
with a custom sizegenerator.generate_n_images(n = 5, foldername= "generated_images", image_size= (700,500))
from devolearn import lineage_population_model
model = lineage_population_model(device = "cpu")
print(model.predict(image_path = "sample_data/images/embryo_sample.png"))
results = model.predict_from_video(video_path = "sample_data/videos/embryo_timelapse.mov", save_csv = True, csv_name = "video_preds.csv", ignore_first_n_frames= 10, ignore_last_n_frames= 10, postprocess = False)
plot = model.create_population_plot_from_video(video_path = "sample_data/videos/embryo_timelapse.mov", save_plot= True, plot_name= "plot.png", ignore_last_n_frames= 0, postprocess = False)
plot.show()
Model | Data source |
---|---|
Segmenting the cell membrane in C. elegans embryo | 3DMMS: robust 3D Membrane Morphological Segmentation of C. elegans embryo |
Segmenting the nucleus in C. elegans embryo | C. elegans Cell-Tracking-Challenge dataset |
Cell lineage population prediction + embryo GAN | EPIC dataset |
Model | Huggingface |
---|---|
Segmenting the cell membrane in C. elegans embryo | Cell Membrane segmentor |
Segmenting the nucleus in C. elegans embryo | C. elegans Nucleus segmentor |
Cell lineage population prediction | Lineage population |
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