Python for Microscopists and other image processing enthusiasts

Author: Dr. Sreenivas Bhattiprolu
Twitter: @digitalsreeni

Python for Microscopists and other image processing enthusiasts

https://www.youtube.com/channel/UC34rW-HtPJulxr5wp2Xa04w?sub_confirmation=1

The YouTube channel associated with this code walks you through the entire process of learning to code in Python; all the way from basics to advanced machine learning and deep learning. The primary emphasis will be on image processing and other relevant functionality.

Why did I create this channel? To help you (students and researchers) gain a new skill and succeed in your respective fields.

You may think coding is hard and that it's not your cup of tea, but Python made it easy to code even advanced algorithms. In addition, coding will make you self sufficient, it will teach you how to think, it improves your collaborative skills and it can take your career to new heights. Therefore, if you want to stay ahead of your peers and relevant in your field, overcome your fears and start coding!

Also, checkout WWW.APEER.COM if you want free image processing in the cloud! Free for non-profits / academics / personal use.

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Python for Microscopists and other image processing enthusiasts

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Name		Name	Last commit message	Last commit date
Latest commit History 227 Commits
222_working_with_large_data_that_does_not_fit_memory_semantic_segm		222_working_with_large_data_that_does_not_fit_memory_semantic_segm
228_semantic_segmentation_of_aerial_imagery_using_unet		228_semantic_segmentation_of_aerial_imagery_using_unet
229_smooth_predictions_by_blending_patches		229_smooth_predictions_by_blending_patches
230_landcover_dataset_segmentation		230_landcover_dataset_segmentation
231_234_BraTa2020_Unet_segmentation		231_234_BraTa2020_Unet_segmentation
235-236_pre-training_unet_using_autoencoders		235-236_pre-training_unet_using_autoencoders
237_tflite_using_malaria_binary_classification		237_tflite_using_malaria_binary_classification
238_face_eye_detection_using_opencv		238_face_eye_detection_using_opencv
239_train_emotion_detection		239_train_emotion_detection
240_train_age_gender_detection		240_train_age_gender_detection
241_live_age_gender_emotion_detection		241_live_age_gender_emotion_detection
images		images
other_files		other_files
00_A review of COVID19 situation in India using Python.py		00_A review of COVID19 situation in India using Python.py
017-Reading_Images_in_Python.py		017-Reading_Images_in_Python.py
018-image_processing_in_pillow.py		018-image_processing_in_pillow.py
019-image_processing_in_scipy.py		019-image_processing_in_scipy.py
020-image_processing_in_scikit-image.py		020-image_processing_in_scikit-image.py
021-scratch_assay_using_scikit_image.py		021-scratch_assay_using_scikit_image.py
022-denoising.py		022-denoising.py
023-histogram_segmentation_using_scikit_image.py		023-histogram_segmentation_using_scikit_image.py
024-random_walker_segmentation_scikit-image.py		024-random_walker_segmentation_scikit-image.py
025-image_processing_in_openCV_intro1-preprocessing.py		025-image_processing_in_openCV_intro1-preprocessing.py
026-image_processing_in_openCV_intro1-preprocessing.py		026-image_processing_in_openCV_intro1-preprocessing.py
027-image_processing_in_openCV_intro2-Thresholding.py		027-image_processing_in_openCV_intro2-Thresholding.py
028-image_processing_in_openCV_intro2-Thresholding.py		028-image_processing_in_openCV_intro2-Thresholding.py
029-keypoint detectors and descriptors in opencv.py		029-keypoint detectors and descriptors in opencv.py
02_Tips_Tricks_python_tips_and_tricks_2_google_image_download.py		02_Tips_Tricks_python_tips_and_tricks_2_google_image_download.py
030-keypoints_homography_for_registration in opencv.py		030-keypoints_homography_for_registration in opencv.py
031-reading_and_writing_csv.py		031-reading_and_writing_csv.py
032-grain_analysis_saving_to_csv.py		032-grain_analysis_saving_to_csv.py
033-grain_size_analysis_using_wateshed_segmentation.py		033-grain_size_analysis_using_wateshed_segmentation.py
034a-grain_size_analysis_using_wateshed_segmentation_multiple_files.py		034a-grain_size_analysis_using_wateshed_segmentation_multiple_files.py
034b-grain_size_analysis_using_wateshed_segmentation_multiple_files_functions.py		034b-grain_size_analysis_using_wateshed_segmentation_multiple_files_functions.py
035-Cell Nuclei analysis using watershed.py		035-Cell Nuclei analysis using watershed.py
036-data_analysis_using_Pandas_Intro_data_loading.py		036-data_analysis_using_Pandas_Intro_data_loading.py
037-data_analysis_using_Pandas_data_handling.py		037-data_analysis_using_Pandas_data_handling.py
038-data_sorting_using_Pandas.py		038-data_sorting_using_Pandas.py
039-data_grouping_using_Pandas.py		039-data_grouping_using_Pandas.py
040-dealing with null data_using_Pandas.py		040-dealing with null data_using_Pandas.py
041_data_analysis_using_Pandas_Plotting.py		041_data_analysis_using_Pandas_Plotting.py
042_data_analysis_using_Seaborn_Plotting.py		042_data_analysis_using_Seaborn_Plotting.py
045-linear_regression_cells.py		045-linear_regression_cells.py
046-linear_regression_cells_train_test.py		046-linear_regression_cells_train_test.py
047-multi_linear_regression.py		047-multi_linear_regression.py
049-Logistic_regression.py		049-Logistic_regression.py
050-K_means_intro.py		050-K_means_intro.py
051-Kmeans_using_opencv.py		051-Kmeans_using_opencv.py
052-GMM_image_segmentation.py		052-GMM_image_segmentation.py
053-How to pick optimal number of parameters.py		053-How to pick optimal number of parameters.py
055-ML_06_01_how to open proprietary images.py		055-ML_06_01_how to open proprietary images.py
057-ML_06_02_what are features.py		057-ML_06_02_what are features.py
058-ML_06_03_what is gabor filter.py		058-ML_06_03_what is gabor filter.py
060-RandomForest1.py		060-RandomForest1.py
061-Gabor_Filter_Banks.py		061-Gabor_Filter_Banks.py
062-066-ML_06_04_TRAIN_ML_segmentation_All_filters_RForest.py		062-066-ML_06_04_TRAIN_ML_segmentation_All_filters_RForest.py
067-ML_06_05_PREDICT_ML_segmentation_All_filters_RForest.py		067-ML_06_05_PREDICT_ML_segmentation_All_filters_RForest.py
068b-ML_06_04_TRAIN_ML_segmentation_All_filters_RForest_SVM.py		068b-ML_06_04_TRAIN_ML_segmentation_All_filters_RForest_SVM.py
069a-Train_BOVW_V1.0.py		069a-Train_BOVW_V1.0.py
069b-Validate_BOVW_V1.0.py		069b-Validate_BOVW_V1.0.py
071-Malaria_cell_CNN_V5.0_for video.py		071-Malaria_cell_CNN_V5.0_for video.py
074-Defining U-net in Python using Keras.py		074-Defining U-net in Python using Keras.py
076-077-078-Unet_nuclei_tutorial.py		076-077-078-Unet_nuclei_tutorial.py
082-docker_test.zip		082-docker_test.zip
085-auto_encode_single_image_V3.0.py		085-auto_encode_single_image_V3.0.py
086--auto_denoise_mnist.py		086--auto_denoise_mnist.py
087-auto_denoise_custom_file_V3.0.py		087-auto_denoise_custom_file_V3.0.py
088-autoencoder_anomaly_V0.1.py		088-autoencoder_anomaly_V0.1.py
089a-auto_encode_single_image_to_different_image_V1.0.py		089a-auto_encode_single_image_to_different_image_V1.0.py
089b-auto_encode_single_image_to_different_image_multi_file_V1.0.py		089b-auto_encode_single_image_to_different_image_multi_file_V1.0.py
090a-autoencoder_colorize_V0.2.py		090a-autoencoder_colorize_V0.2.py
090b-autoencoder_colorize_V0.1_predict.py		090b-autoencoder_colorize_V0.1_predict.py
091_intro_to_transfer_learning_VGG16.py		091_intro_to_transfer_learning_VGG16.py
092-autoencoder_colorize_transfer_learning_VGG16_V0.1.py		092-autoencoder_colorize_transfer_learning_VGG16_V0.1.py
093_no_need_for_deep_learning.py		093_no_need_for_deep_learning.py
094_denoising_MRI.py		094_denoising_MRI.py
095_what_is_convolution.py		095_what_is_convolution.py
096_What is Gaussian denoising.py		096_What is Gaussian denoising.py
097_What is Median denoising.py		097_What is Median denoising.py
098_What is Bilateral denoising.py		098_What is Bilateral denoising.py
099_WHat is NLM.py		099_WHat is NLM.py
100_What is Total Variation denoising.py		100_What is Total Variation denoising.py
101-What is BM3D.py		101-What is BM3D.py
102-What is Unsharp Mask.py		102-What is Unsharp Mask.py
103_edge_filters.py		103_edge_filters.py
104_ridge_filters.py		104_ridge_filters.py
105_what_is_fourier_transform.py		105_what_is_fourier_transform.py
106_image_filters_using_fourier_transform_DFT.py		106_image_filters_using_fourier_transform_DFT.py
107_analysis_of_covid19_data_using_python_part1.py		107_analysis_of_covid19_data_using_python_part1.py
108_analysis_of_covid19_data_using_python_part2.py		108_analysis_of_covid19_data_using_python_part2.py
109_.predicting_covid19_cases_using_pythonpy.py		109_.predicting_covid19_cases_using_pythonpy.py
110_covid19_visualization_using_plotly.py		110_covid19_visualization_using_plotly.py
111_top_10_countries_with_highest_cases_deaths.py		111_top_10_countries_with_highest_cases_deaths.py
112_denoising_images_by_dct_averaging.py		112_denoising_images_by_dct_averaging.py
113-what_is_histogram_equalization.py		113-what_is_histogram_equalization.py
114_auto_image_quality_assessment_BRISQUE.py		114_auto_image_quality_assessment_BRISQUE.py
115_auto_segmentation_using_multiotsu.py		115_auto_segmentation_using_multiotsu.py
116_.measuring_properties_of_labeled_objects_in_imagespy.py		116_.measuring_properties_of_labeled_objects_in_imagespy.py
117_shading_correction_using_rolling_ball.py		117_shading_correction_using_rolling_ball.py
118_object_detection_by_template_matching.py		118_object_detection_by_template_matching.py

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