spacr 0.9.26__tar.gz → 1.0.0__tar.gz

{spacr-0.9.26/spacr.egg-info → spacr-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.26
+Version: 1.0.0
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -13,7 +13,8 @@ License-File: LICENSE
 Requires-Dist: numpy<2.0,>=1.26.4
 Requires-Dist: pandas<3.0,>=2.2.1
 Requires-Dist: scipy<2.0,>=1.12.0
-Requires-Dist: cellpose<4.0,>=3.0.6
+Requires-Dist: cellpose<5.0,>=4.0
+Requires-Dist: segment-anything
 Requires-Dist: scikit-image<1.0,>=0.22.0
 Requires-Dist: scikit-learn<2.0,>=1.4.1
 Requires-Dist: scikit-posthocs<0.20,>=0.10.0
@@ -195,6 +196,13 @@ The following example Jupyter notebooks illustrate common workflows using spaCR.
 - `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_  
   *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
 
+Interactive Tutorial (under construction)
+-----------------------------------------
+
+Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
+
+`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+
 License
 -------
 spaCR is distributed under the terms of the MIT License.

{spacr-0.9.26 → spacr-1.0.0}/README.rst

@@ -113,6 +113,13 @@ The following example Jupyter notebooks illustrate common workflows using spaCR.
 - `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_  
   *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
 
+Interactive Tutorial (under construction)
+-----------------------------------------
+
+Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
+
+`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+
 License
 -------
 spaCR is distributed under the terms of the MIT License.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_00_code.txt

@@ -0,0 +1,37 @@
+from spacr.core import preprocess_generate_masks
+%matplotlib inline
+
+settings = {'src':'/home/olafsson/datasets/plate1', # (path) path to source folder (where origional images were stored)
+            'metadata_type':'cellvoyager', # (string) - type of fime name metadata (cellvoyager, cq1, Nikon)
+            'custom_regex':None, # (regex) - Regular expression if filename metadata not in metadata_type 
+            'experiment':'screen', # (string) - Name of experiment
+            'channels':[0,1,2,3], # (list) - list of integers representing available channels
+            'cell_channel':3, # (integer or NoneType) - Cell image dimension 
+            'cell_background':100, # (integer) - Background value in cell images
+            'cell_Signal_to_noise':10, # (integer) - Signal to noise ration for cell channel
+            'cell_CP_prob':-1, # (integer) - Cellpose Cell probability
+            'remove_background_cell':False, # (bool) - Set background to 0 for cell channel
+            'nucleus_channel':0, # (Optional, integer or NoneType) - Nucleus image dimension 
+            'nucleus_background':200, # (Optional, integer) - Background value in nucleus images
+            'nucleus_Signal_to_noise':5, # (Optional, integer) - Signal to noise ration for nucleus channel
+            'nucleus_CP_prob':0, # (Optional, integer) - Cellpose Nucleus probability
+            'remove_background_nucleus':False, # (Optional, bool) - Set background to 0 for nucleus channel
+            'pathogen_model':None, # (Optional, path or NoneType) - Custom cellpose model path for pathogen detection
+            'pathogen_channel':2, # (Optional, integer or NoneType) - Pathogen image dimension 
+            'pathogen_background':400, # (Optional, integer) - Background value in pathogen images
+            'pathogen_Signal_to_noise':5, # (Optional, integer) - Signal to noise ration for pathogen channel
+            'pathogen_CP_prob':-2, # (Optional, integer) - Cellpose pathogen probability
+            'remove_background_pathogen':True, # (Optional, bool) - Set background to 0 for pathogen channel
+            'consolidate':False, # (Optional, bool) - Consolidate files from multilevel folderstructure into one folder.
+            'magnification':40, # (integer) - Objective magnefication used to aquire images (40, 60, 100)
+            'save':True, # (bool) - Save masks and object data to database
+            'preprocess':True, # (bool) - Preprocess images
+            'masks':True, # (bool) - Generate masks
+            'batch_size':50, # (bool) - Number of images to be normalized together and loaded onto the GPU
+            'filter':False, # (bool) - Filter objects based on size
+            'merge_pathogens':False, # (bool) - Merge pathogens that share > 75% perimiter
+            'plot':True, # (bool) - Plot normalized intensity and object images
+            'adjust_cells':True, # (bool) - If cell, nucleus and pathogen: merge cells that share a pathogen
+            'test_mode':True, # (bool) - Test settings in test mode before analyzing entire experiment
+            'test_images':10, # (integer) - Number of images to analyze in test mode
+            'random_test':True} # (bool) - Randomize images for test mode

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_code.txt

@@ -0,0 +1 @@
+preprocess_generate_masks(settings)

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_00_text.txt

@@ -0,0 +1,3 @@
+Processing folder: /home/olafsson/datasets/plate1
+Found path: /home/olafsson/datasets/plate1
+Saving settings to /home/olafsson/datasets/plate1/settings/gen_mask_settings.csv

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_02_text.txt

@@ -0,0 +1,63 @@
+Starting Test mode ...
+Found 208 tif files
+Image_format: tif
+regex mode:cellvoyager regex:(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*).tif
+Running spacr in test mode
+Found 208 files
+Using 10 random image set(s) for test model
+All files: 40 in /home/olafsson/datasets/plate1/test
+All unique FOV: 40 in /home/olafsson/datasets/plate1/test
+Progress: 1/40, operation_type: Preprocessing filenames, Time/batch: 0.434sec, Time/image: 0.009sec, Time_left: 0.282 min.
+Progress: 2/40, operation_type: Preprocessing filenames, Time/batch: 0.440sec, Time/image: 0.009sec, Time_left: 0.279 min.
+Progress: 3/40, operation_type: Preprocessing filenames, Time/batch: 0.444sec, Time/image: 0.009sec, Time_left: 0.274 min.
+Progress: 4/40, operation_type: Preprocessing filenames, Time/batch: 0.448sec, Time/image: 0.009sec, Time_left: 0.269 min.
+Progress: 5/40, operation_type: Preprocessing filenames, Time/batch: 0.451sec, Time/image: 0.009sec, Time_left: 0.263 min.
+Progress: 6/40, operation_type: Preprocessing filenames, Time/batch: 0.454sec, Time/image: 0.009sec, Time_left: 0.257 min.
+Progress: 7/40, operation_type: Preprocessing filenames, Time/batch: 0.457sec, Time/image: 0.009sec, Time_left: 0.251 min.
+Progress: 8/40, operation_type: Preprocessing filenames, Time/batch: 0.460sec, Time/image: 0.009sec, Time_left: 0.245 min.
+Progress: 9/40, operation_type: Preprocessing filenames, Time/batch: 0.463sec, Time/image: 0.009sec, Time_left: 0.239 min.
+Progress: 10/40, operation_type: Preprocessing filenames, Time/batch: 0.466sec, Time/image: 0.009sec, Time_left: 0.233 min.
+Progress: 11/40, operation_type: Preprocessing filenames, Time/batch: 0.469sec, Time/image: 0.009sec, Time_left: 0.227 min.
+Progress: 12/40, operation_type: Preprocessing filenames, Time/batch: 0.472sec, Time/image: 0.009sec, Time_left: 0.220 min.
+Progress: 13/40, operation_type: Preprocessing filenames, Time/batch: 0.475sec, Time/image: 0.010sec, Time_left: 0.214 min.
+Progress: 14/40, operation_type: Preprocessing filenames, Time/batch: 0.478sec, Time/image: 0.010sec, Time_left: 0.207 min.
+Progress: 15/40, operation_type: Preprocessing filenames, Time/batch: 0.481sec, Time/image: 0.010sec, Time_left: 0.200 min.
+Progress: 16/40, operation_type: Preprocessing filenames, Time/batch: 0.484sec, Time/image: 0.010sec, Time_left: 0.194 min.
+Progress: 17/40, operation_type: Preprocessing filenames, Time/batch: 0.487sec, Time/image: 0.010sec, Time_left: 0.187 min.
+Progress: 18/40, operation_type: Preprocessing filenames, Time/batch: 0.490sec, Time/image: 0.010sec, Time_left: 0.180 min.
+Progress: 19/40, operation_type: Preprocessing filenames, Time/batch: 0.493sec, Time/image: 0.010sec, Time_left: 0.172 min.
+Progress: 20/40, operation_type: Preprocessing filenames, Time/batch: 0.495sec, Time/image: 0.010sec, Time_left: 0.165 min.
+Progress: 21/40, operation_type: Preprocessing filenames, Time/batch: 0.498sec, Time/image: 0.010sec, Time_left: 0.158 min.
+Progress: 22/40, operation_type: Preprocessing filenames, Time/batch: 0.501sec, Time/image: 0.010sec, Time_left: 0.150 min.
+Progress: 23/40, operation_type: Preprocessing filenames, Time/batch: 0.504sec, Time/image: 0.010sec, Time_left: 0.143 min.
+Progress: 24/40, operation_type: Preprocessing filenames, Time/batch: 0.507sec, Time/image: 0.010sec, Time_left: 0.135 min.
+Progress: 25/40, operation_type: Preprocessing filenames, Time/batch: 0.510sec, Time/image: 0.010sec, Time_left: 0.127 min.
+Progress: 26/40, operation_type: Preprocessing filenames, Time/batch: 0.513sec, Time/image: 0.010sec, Time_left: 0.120 min.
+Progress: 27/40, operation_type: Preprocessing filenames, Time/batch: 0.516sec, Time/image: 0.010sec, Time_left: 0.112 min.
+Progress: 28/40, operation_type: Preprocessing filenames, Time/batch: 0.518sec, Time/image: 0.010sec, Time_left: 0.104 min.
+Progress: 29/40, operation_type: Preprocessing filenames, Time/batch: 0.521sec, Time/image: 0.010sec, Time_left: 0.096 min.
+Progress: 30/40, operation_type: Preprocessing filenames, Time/batch: 0.524sec, Time/image: 0.010sec, Time_left: 0.087 min.
+Progress: 31/40, operation_type: Preprocessing filenames, Time/batch: 0.527sec, Time/image: 0.011sec, Time_left: 0.079 min.
+Progress: 32/40, operation_type: Preprocessing filenames, Time/batch: 0.530sec, Time/image: 0.011sec, Time_left: 0.071 min.
+Progress: 33/40, operation_type: Preprocessing filenames, Time/batch: 0.533sec, Time/image: 0.011sec, Time_left: 0.062 min.
+Progress: 34/40, operation_type: Preprocessing filenames, Time/batch: 0.536sec, Time/image: 0.011sec, Time_left: 0.054 min.
+Progress: 35/40, operation_type: Preprocessing filenames, Time/batch: 0.538sec, Time/image: 0.011sec, Time_left: 0.045 min.
+Progress: 36/40, operation_type: Preprocessing filenames, Time/batch: 0.541sec, Time/image: 0.011sec, Time_left: 0.036 min.
+Progress: 37/40, operation_type: Preprocessing filenames, Time/batch: 0.544sec, Time/image: 0.011sec, Time_left: 0.027 min.
+Progress: 38/40, operation_type: Preprocessing filenames, Time/batch: 0.547sec, Time/image: 0.011sec, Time_left: 0.018 min.
+Progress: 39/40, operation_type: Preprocessing filenames, Time/batch: 0.550sec, Time/image: 0.011sec, Time_left: 0.009 min.
+Progress: 40/40, operation_type: Preprocessing filenames, Time/batch: 0.553sec, Time/image: 0.011sec, Time_left: 0.000 min.
+List of folders in src: ['1', '2', '3', '4']. Single channel folders.
+Generated folder with merged arrays: /home/olafsson/datasets/plate1/test/stack
+Progress: 1/10, operation_type: Merging channels into npy stacks, Time/image: 0.220sec, Time_left: 0.033 min.
+Progress: 2/10, operation_type: Merging channels into npy stacks, Time/image: 0.209sec, Time_left: 0.028 min.
+Progress: 3/10, operation_type: Merging channels into npy stacks, Time/image: 0.205sec, Time_left: 0.024 min.
+Progress: 4/10, operation_type: Merging channels into npy stacks, Time/image: 0.201sec, Time_left: 0.020 min.
+Progress: 5/10, operation_type: Merging channels into npy stacks, Time/image: 0.197sec, Time_left: 0.016 min.
+Progress: 6/10, operation_type: Merging channels into npy stacks, Time/image: 0.198sec, Time_left: 0.013 min.
+Progress: 7/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.010 min.
+Progress: 8/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.007 min.
+Progress: 9/10, operation_type: Merging channels into npy stacks, Time/image: 0.195sec, Time_left: 0.003 min.
+Progress: 10/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.000 min.
+plotting 1 images from /home/olafsson/datasets/plate1/test/stack
+Image path:/home/olafsson/datasets/plate1/test/stack/plate1_E02_21_1.npy

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_04_text.txt

@@ -0,0 +1,20 @@
+Progress: 1/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.001 min.
+Progress: 2/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.001 min.
+Progress: 3/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.001 min.
+Progress: 4/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.000 min.
+Progress: 5/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.000 min.
+Progress: 6/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.000 min.
+Progress: 7/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.000 min.
+Progress: 8/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.000 min.
+Progress: 9/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.000 min.
+Progress: 10/10, operation_type: Concatinating, Time/image: 0.005sec, Time_left: 0.000 min.
+Processing channel 0: background=200, signal_threshold=1000, remove_background=False
+Channel 0: global_lower=12.0, global_upper=3825.0, Signal-to-noise=318.75
+Progress: 1/3, operation_type: Normalizing, Time/image: 0.697sec, Time_left: 0.023 min.
+Processing channel 3: background=100, signal_threshold=1000, remove_background=False
+Channel 3: global_lower=113.0, global_upper=2195.0, Signal-to-noise=19.424778761061948
+Progress: 2/3, operation_type: Normalizing, Time/image: 0.636sec, Time_left: 0.011 min.
+Processing channel 2: background=400, signal_threshold=2000, remove_background=True
+Channel 2: global_lower=423.0, global_upper=6262.0, Signal-to-noise=14.803782505910165
+Progress: 3/3, operation_type: Normalizing, Time/image: 0.518sec, Time_left: 0.000 min.
+All files concatenated and normalized. Saved to: /home/olafsson/datasets/plate1/test/masks

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_06_text.txt

@@ -0,0 +1,4 @@
+{'diameter': 160, 'minimum_size': 6400.0, 'maximum_size': 256000, 'merge': False, 'resample': True, 'remove_border_objects': False, 'model_name': 'cyto2', 'filter_size': False, 'filter_intensity': False, 'restore_type': None}
+{'nucleus': [0, 0], 'pathogen': [0, 2], 'cell': [0, 1]}
+Device 0: NVIDIA GeForce RTX 3090, VRAM: 23.56 GB, cellpose batch size: 48
+Number of objects, : 27

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_08_text.txt

@@ -0,0 +1 @@
+object_size:cell: 17147.916 px2

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_19_text.txt

@@ -0,0 +1 @@
+Progress: 1/3, operation_type: cell_mask_gen, Time/image: 35.657sec, Time_left: 1.189 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_21_text.txt

@@ -0,0 +1,4 @@
+{'diameter': 75, 'minimum_size': 1406.25, 'maximum_size': 56250, 'merge': False, 'resample': True, 'remove_border_objects': False, 'model_name': 'nuclei', 'filter_size': False, 'filter_intensity': False, 'restore_type': None}
+{'nucleus': [0, 0], 'pathogen': [0, 2], 'cell': [0, 1]}
+Device 0: NVIDIA GeForce RTX 3090, VRAM: 23.56 GB, cellpose batch size: 48
+Number of objects, : 34

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_23_text.txt

@@ -0,0 +1 @@
+object_size:nucleus: 6683.251 px2

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_34_text.txt

@@ -0,0 +1 @@
+Progress: 2/3, operation_type: nucleus_mask_gen, Time/image: 23.892sec, Time_left: 0.398 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_36_text.txt

@@ -0,0 +1,4 @@
+{'diameter': 40, 'minimum_size': 400.0, 'maximum_size': 16000, 'merge': False, 'resample': False, 'remove_border_objects': False, 'model_name': 'cyto', 'filter_size': False, 'filter_intensity': False, 'restore_type': None}
+{'nucleus': [0, 0], 'pathogen': [0, 2], 'cell': [0, 1]}
+Device 0: NVIDIA GeForce RTX 3090, VRAM: 23.56 GB, cellpose batch size: 48
+Number of objects, : 22

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_38_text.txt

@@ -0,0 +1 @@
+object_size:pathogen: 1697.431 px2

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_49_text.txt

@@ -0,0 +1,23 @@
+Progress: 3/3, operation_type: pathogen_mask_gen, Time/image: 19.432sec, Time_left: 0.000 min.
+Adjusting cell masks with nuclei and pathogen masks
+Progress: 1/10, operation_type: adjust_cell_masks, Time/image: 0.422sec, Time_left: 0.063 min.
+Progress: 2/10, operation_type: adjust_cell_masks, Time/image: 0.581sec, Time_left: 0.077 min.
+Progress: 3/10, operation_type: adjust_cell_masks, Time/image: 0.486sec, Time_left: 0.057 min.
+Progress: 4/10, operation_type: adjust_cell_masks, Time/image: 0.601sec, Time_left: 0.060 min.
+Progress: 5/10, operation_type: adjust_cell_masks, Time/image: 0.532sec, Time_left: 0.044 min.
+Progress: 6/10, operation_type: adjust_cell_masks, Time/image: 0.566sec, Time_left: 0.038 min.
+Progress: 7/10, operation_type: adjust_cell_masks, Time/image: 0.577sec, Time_left: 0.029 min.
+Progress: 8/10, operation_type: adjust_cell_masks, Time/image: 0.575sec, Time_left: 0.019 min.
+Progress: 9/10, operation_type: adjust_cell_masks, Time/image: 0.569sec, Time_left: 0.009 min.
+Progress: 10/10, operation_type: adjust_cell_masks, Time/image: 0.577sec, Time_left: 0.000 min.
+Cell mask adjustment: 0.09624974330266317 min.
+Progress: 1/10, operation_type: Merging Arrays, Time/image: 0.076sec, Time_left: 0.011 min.
+Progress: 2/10, operation_type: Merging Arrays, Time/image: 0.077sec, Time_left: 0.010 min.
+Progress: 3/10, operation_type: Merging Arrays, Time/image: 0.076sec, Time_left: 0.009 min.
+Progress: 4/10, operation_type: Merging Arrays, Time/image: 0.076sec, Time_left: 0.008 min.
+Progress: 5/10, operation_type: Merging Arrays, Time/image: 0.076sec, Time_left: 0.006 min.
+Progress: 6/10, operation_type: Merging Arrays, Time/image: 0.076sec, Time_left: 0.005 min.
+Progress: 7/10, operation_type: Merging Arrays, Time/image: 0.076sec, Time_left: 0.004 min.
+Progress: 8/10, operation_type: Merging Arrays, Time/image: 0.075sec, Time_left: 0.003 min.
+Progress: 9/10, operation_type: Merging Arrays, Time/image: 0.075sec, Time_left: 0.001 min.
+Progress: 10/10, operation_type: Merging Arrays, Time/image: 0.075sec, Time_left: 0.000 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_51_text.txt

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+Progress: 1/42, operation_type: Plot mask outlines, Time/image: 3.719sec, Time_left: 2.541 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_53_text.txt

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+Progress: 2/42, operation_type: Plot mask outlines, Time/image: 3.673sec, Time_left: 2.448 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_55_text.txt

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+Progress: 3/42, operation_type: Plot mask outlines, Time/image: 3.658sec, Time_left: 2.378 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_57_text.txt

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+Progress: 4/42, operation_type: Plot mask outlines, Time/image: 3.621sec, Time_left: 2.294 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_59_text.txt

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+Progress: 5/42, operation_type: Plot mask outlines, Time/image: 3.601sec, Time_left: 2.220 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_61_text.txt

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+Progress: 6/42, operation_type: Plot mask outlines, Time/image: 3.599sec, Time_left: 2.160 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_63_text.txt

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+Progress: 7/42, operation_type: Plot mask outlines, Time/image: 3.620sec, Time_left: 2.112 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_65_text.txt

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+Progress: 8/42, operation_type: Plot mask outlines, Time/image: 3.613sec, Time_left: 2.047 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_67_text.txt

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+Progress: 9/42, operation_type: Plot mask outlines, Time/image: 3.600sec, Time_left: 1.980 min.

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/cell_01_out_69_text.txt

@@ -0,0 +1,2 @@
+Progress: 10/42, operation_type: Plot mask outlines, Time/image: 3.597sec, Time_left: 1.919 min.
+Successfully completed run

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/console_output.js

@@ -0,0 +1,63 @@
+Starting Test mode ...
+Found 208 tif files
+Image_format: tif
+regex mode:cellvoyager regex:(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*).tif
+Running spacr in test mode
+Found 208 files
+Using 10 random image set(s) for test model
+All files: 40 in /home/olafsson/datasets/plate1/test
+All unique FOV: 40 in /home/olafsson/datasets/plate1/test
+Progress: 1/40, operation_type: Preprocessing filenames, Time/batch: 0.434sec, Time/image: 0.009sec, Time_left: 0.282 min.
+Progress: 2/40, operation_type: Preprocessing filenames, Time/batch: 0.440sec, Time/image: 0.009sec, Time_left: 0.279 min.
+Progress: 3/40, operation_type: Preprocessing filenames, Time/batch: 0.444sec, Time/image: 0.009sec, Time_left: 0.274 min.
+Progress: 4/40, operation_type: Preprocessing filenames, Time/batch: 0.448sec, Time/image: 0.009sec, Time_left: 0.269 min.
+Progress: 5/40, operation_type: Preprocessing filenames, Time/batch: 0.451sec, Time/image: 0.009sec, Time_left: 0.263 min.
+Progress: 6/40, operation_type: Preprocessing filenames, Time/batch: 0.454sec, Time/image: 0.009sec, Time_left: 0.257 min.
+Progress: 7/40, operation_type: Preprocessing filenames, Time/batch: 0.457sec, Time/image: 0.009sec, Time_left: 0.251 min.
+Progress: 8/40, operation_type: Preprocessing filenames, Time/batch: 0.460sec, Time/image: 0.009sec, Time_left: 0.245 min.
+Progress: 9/40, operation_type: Preprocessing filenames, Time/batch: 0.463sec, Time/image: 0.009sec, Time_left: 0.239 min.
+Progress: 10/40, operation_type: Preprocessing filenames, Time/batch: 0.466sec, Time/image: 0.009sec, Time_left: 0.233 min.
+Progress: 11/40, operation_type: Preprocessing filenames, Time/batch: 0.469sec, Time/image: 0.009sec, Time_left: 0.227 min.
+Progress: 12/40, operation_type: Preprocessing filenames, Time/batch: 0.472sec, Time/image: 0.009sec, Time_left: 0.220 min.
+Progress: 13/40, operation_type: Preprocessing filenames, Time/batch: 0.475sec, Time/image: 0.010sec, Time_left: 0.214 min.
+Progress: 14/40, operation_type: Preprocessing filenames, Time/batch: 0.478sec, Time/image: 0.010sec, Time_left: 0.207 min.
+Progress: 15/40, operation_type: Preprocessing filenames, Time/batch: 0.481sec, Time/image: 0.010sec, Time_left: 0.200 min.
+Progress: 16/40, operation_type: Preprocessing filenames, Time/batch: 0.484sec, Time/image: 0.010sec, Time_left: 0.194 min.
+Progress: 17/40, operation_type: Preprocessing filenames, Time/batch: 0.487sec, Time/image: 0.010sec, Time_left: 0.187 min.
+Progress: 18/40, operation_type: Preprocessing filenames, Time/batch: 0.490sec, Time/image: 0.010sec, Time_left: 0.180 min.
+Progress: 19/40, operation_type: Preprocessing filenames, Time/batch: 0.493sec, Time/image: 0.010sec, Time_left: 0.172 min.
+Progress: 20/40, operation_type: Preprocessing filenames, Time/batch: 0.495sec, Time/image: 0.010sec, Time_left: 0.165 min.
+Progress: 21/40, operation_type: Preprocessing filenames, Time/batch: 0.498sec, Time/image: 0.010sec, Time_left: 0.158 min.
+Progress: 22/40, operation_type: Preprocessing filenames, Time/batch: 0.501sec, Time/image: 0.010sec, Time_left: 0.150 min.
+Progress: 23/40, operation_type: Preprocessing filenames, Time/batch: 0.504sec, Time/image: 0.010sec, Time_left: 0.143 min.
+Progress: 24/40, operation_type: Preprocessing filenames, Time/batch: 0.507sec, Time/image: 0.010sec, Time_left: 0.135 min.
+Progress: 25/40, operation_type: Preprocessing filenames, Time/batch: 0.510sec, Time/image: 0.010sec, Time_left: 0.127 min.
+Progress: 26/40, operation_type: Preprocessing filenames, Time/batch: 0.513sec, Time/image: 0.010sec, Time_left: 0.120 min.
+Progress: 27/40, operation_type: Preprocessing filenames, Time/batch: 0.516sec, Time/image: 0.010sec, Time_left: 0.112 min.
+Progress: 28/40, operation_type: Preprocessing filenames, Time/batch: 0.518sec, Time/image: 0.010sec, Time_left: 0.104 min.
+Progress: 29/40, operation_type: Preprocessing filenames, Time/batch: 0.521sec, Time/image: 0.010sec, Time_left: 0.096 min.
+Progress: 30/40, operation_type: Preprocessing filenames, Time/batch: 0.524sec, Time/image: 0.010sec, Time_left: 0.087 min.
+Progress: 31/40, operation_type: Preprocessing filenames, Time/batch: 0.527sec, Time/image: 0.011sec, Time_left: 0.079 min.
+Progress: 32/40, operation_type: Preprocessing filenames, Time/batch: 0.530sec, Time/image: 0.011sec, Time_left: 0.071 min.
+Progress: 33/40, operation_type: Preprocessing filenames, Time/batch: 0.533sec, Time/image: 0.011sec, Time_left: 0.062 min.
+Progress: 34/40, operation_type: Preprocessing filenames, Time/batch: 0.536sec, Time/image: 0.011sec, Time_left: 0.054 min.
+Progress: 35/40, operation_type: Preprocessing filenames, Time/batch: 0.538sec, Time/image: 0.011sec, Time_left: 0.045 min.
+Progress: 36/40, operation_type: Preprocessing filenames, Time/batch: 0.541sec, Time/image: 0.011sec, Time_left: 0.036 min.
+Progress: 37/40, operation_type: Preprocessing filenames, Time/batch: 0.544sec, Time/image: 0.011sec, Time_left: 0.027 min.
+Progress: 38/40, operation_type: Preprocessing filenames, Time/batch: 0.547sec, Time/image: 0.011sec, Time_left: 0.018 min.
+Progress: 39/40, operation_type: Preprocessing filenames, Time/batch: 0.550sec, Time/image: 0.011sec, Time_left: 0.009 min.
+Progress: 40/40, operation_type: Preprocessing filenames, Time/batch: 0.553sec, Time/image: 0.011sec, Time_left: 0.000 min.
+List of folders in src: ['1', '2', '3', '4']. Single channel folders.
+Generated folder with merged arrays: /home/olafsson/datasets/plate1/test/stack
+Progress: 1/10, operation_type: Merging channels into npy stacks, Time/image: 0.220sec, Time_left: 0.033 min.
+Progress: 2/10, operation_type: Merging channels into npy stacks, Time/image: 0.209sec, Time_left: 0.028 min.
+Progress: 3/10, operation_type: Merging channels into npy stacks, Time/image: 0.205sec, Time_left: 0.024 min.
+Progress: 4/10, operation_type: Merging channels into npy stacks, Time/image: 0.201sec, Time_left: 0.020 min.
+Progress: 5/10, operation_type: Merging channels into npy stacks, Time/image: 0.197sec, Time_left: 0.016 min.
+Progress: 6/10, operation_type: Merging channels into npy stacks, Time/image: 0.198sec, Time_left: 0.013 min.
+Progress: 7/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.010 min.
+Progress: 8/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.007 min.
+Progress: 9/10, operation_type: Merging channels into npy stacks, Time/image: 0.195sec, Time_left: 0.003 min.
+Progress: 10/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.000 min.
+plotting 1 images from /home/olafsson/datasets/plate1/test/stack
+Image path:/home/olafsson/datasets/plate1/test/stack/plate1_E02_21_1.npy

spacr-1.0.0/docs/resources/tutorial/1_mask/notebook/console_output.txt

@@ -0,0 +1,63 @@
+Starting Test mode ...
+Found 208 tif files
+Image_format: tif
+regex mode:cellvoyager regex:(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*).tif
+Running spacr in test mode
+Found 208 files
+Using 10 random image set(s) for test model
+All files: 40 in /home/olafsson/datasets/plate1/test
+All unique FOV: 40 in /home/olafsson/datasets/plate1/test
+Progress: 1/40, operation_type: Preprocessing filenames, Time/batch: 0.434sec, Time/image: 0.009sec, Time_left: 0.282 min.
+Progress: 2/40, operation_type: Preprocessing filenames, Time/batch: 0.440sec, Time/image: 0.009sec, Time_left: 0.279 min.
+Progress: 3/40, operation_type: Preprocessing filenames, Time/batch: 0.444sec, Time/image: 0.009sec, Time_left: 0.274 min.
+Progress: 4/40, operation_type: Preprocessing filenames, Time/batch: 0.448sec, Time/image: 0.009sec, Time_left: 0.269 min.
+Progress: 5/40, operation_type: Preprocessing filenames, Time/batch: 0.451sec, Time/image: 0.009sec, Time_left: 0.263 min.
+Progress: 6/40, operation_type: Preprocessing filenames, Time/batch: 0.454sec, Time/image: 0.009sec, Time_left: 0.257 min.
+Progress: 7/40, operation_type: Preprocessing filenames, Time/batch: 0.457sec, Time/image: 0.009sec, Time_left: 0.251 min.
+Progress: 8/40, operation_type: Preprocessing filenames, Time/batch: 0.460sec, Time/image: 0.009sec, Time_left: 0.245 min.
+Progress: 9/40, operation_type: Preprocessing filenames, Time/batch: 0.463sec, Time/image: 0.009sec, Time_left: 0.239 min.
+Progress: 10/40, operation_type: Preprocessing filenames, Time/batch: 0.466sec, Time/image: 0.009sec, Time_left: 0.233 min.
+Progress: 11/40, operation_type: Preprocessing filenames, Time/batch: 0.469sec, Time/image: 0.009sec, Time_left: 0.227 min.
+Progress: 12/40, operation_type: Preprocessing filenames, Time/batch: 0.472sec, Time/image: 0.009sec, Time_left: 0.220 min.
+Progress: 13/40, operation_type: Preprocessing filenames, Time/batch: 0.475sec, Time/image: 0.010sec, Time_left: 0.214 min.
+Progress: 14/40, operation_type: Preprocessing filenames, Time/batch: 0.478sec, Time/image: 0.010sec, Time_left: 0.207 min.
+Progress: 15/40, operation_type: Preprocessing filenames, Time/batch: 0.481sec, Time/image: 0.010sec, Time_left: 0.200 min.
+Progress: 16/40, operation_type: Preprocessing filenames, Time/batch: 0.484sec, Time/image: 0.010sec, Time_left: 0.194 min.
+Progress: 17/40, operation_type: Preprocessing filenames, Time/batch: 0.487sec, Time/image: 0.010sec, Time_left: 0.187 min.
+Progress: 18/40, operation_type: Preprocessing filenames, Time/batch: 0.490sec, Time/image: 0.010sec, Time_left: 0.180 min.
+Progress: 19/40, operation_type: Preprocessing filenames, Time/batch: 0.493sec, Time/image: 0.010sec, Time_left: 0.172 min.
+Progress: 20/40, operation_type: Preprocessing filenames, Time/batch: 0.495sec, Time/image: 0.010sec, Time_left: 0.165 min.
+Progress: 21/40, operation_type: Preprocessing filenames, Time/batch: 0.498sec, Time/image: 0.010sec, Time_left: 0.158 min.
+Progress: 22/40, operation_type: Preprocessing filenames, Time/batch: 0.501sec, Time/image: 0.010sec, Time_left: 0.150 min.
+Progress: 23/40, operation_type: Preprocessing filenames, Time/batch: 0.504sec, Time/image: 0.010sec, Time_left: 0.143 min.
+Progress: 24/40, operation_type: Preprocessing filenames, Time/batch: 0.507sec, Time/image: 0.010sec, Time_left: 0.135 min.
+Progress: 25/40, operation_type: Preprocessing filenames, Time/batch: 0.510sec, Time/image: 0.010sec, Time_left: 0.127 min.
+Progress: 26/40, operation_type: Preprocessing filenames, Time/batch: 0.513sec, Time/image: 0.010sec, Time_left: 0.120 min.
+Progress: 27/40, operation_type: Preprocessing filenames, Time/batch: 0.516sec, Time/image: 0.010sec, Time_left: 0.112 min.
+Progress: 28/40, operation_type: Preprocessing filenames, Time/batch: 0.518sec, Time/image: 0.010sec, Time_left: 0.104 min.
+Progress: 29/40, operation_type: Preprocessing filenames, Time/batch: 0.521sec, Time/image: 0.010sec, Time_left: 0.096 min.
+Progress: 30/40, operation_type: Preprocessing filenames, Time/batch: 0.524sec, Time/image: 0.010sec, Time_left: 0.087 min.
+Progress: 31/40, operation_type: Preprocessing filenames, Time/batch: 0.527sec, Time/image: 0.011sec, Time_left: 0.079 min.
+Progress: 32/40, operation_type: Preprocessing filenames, Time/batch: 0.530sec, Time/image: 0.011sec, Time_left: 0.071 min.
+Progress: 33/40, operation_type: Preprocessing filenames, Time/batch: 0.533sec, Time/image: 0.011sec, Time_left: 0.062 min.
+Progress: 34/40, operation_type: Preprocessing filenames, Time/batch: 0.536sec, Time/image: 0.011sec, Time_left: 0.054 min.
+Progress: 35/40, operation_type: Preprocessing filenames, Time/batch: 0.538sec, Time/image: 0.011sec, Time_left: 0.045 min.
+Progress: 36/40, operation_type: Preprocessing filenames, Time/batch: 0.541sec, Time/image: 0.011sec, Time_left: 0.036 min.
+Progress: 37/40, operation_type: Preprocessing filenames, Time/batch: 0.544sec, Time/image: 0.011sec, Time_left: 0.027 min.
+Progress: 38/40, operation_type: Preprocessing filenames, Time/batch: 0.547sec, Time/image: 0.011sec, Time_left: 0.018 min.
+Progress: 39/40, operation_type: Preprocessing filenames, Time/batch: 0.550sec, Time/image: 0.011sec, Time_left: 0.009 min.
+Progress: 40/40, operation_type: Preprocessing filenames, Time/batch: 0.553sec, Time/image: 0.011sec, Time_left: 0.000 min.
+List of folders in src: ['1', '2', '3', '4']. Single channel folders.
+Generated folder with merged arrays: /home/olafsson/datasets/plate1/test/stack
+Progress: 1/10, operation_type: Merging channels into npy stacks, Time/image: 0.220sec, Time_left: 0.033 min.
+Progress: 2/10, operation_type: Merging channels into npy stacks, Time/image: 0.209sec, Time_left: 0.028 min.
+Progress: 3/10, operation_type: Merging channels into npy stacks, Time/image: 0.205sec, Time_left: 0.024 min.
+Progress: 4/10, operation_type: Merging channels into npy stacks, Time/image: 0.201sec, Time_left: 0.020 min.
+Progress: 5/10, operation_type: Merging channels into npy stacks, Time/image: 0.197sec, Time_left: 0.016 min.
+Progress: 6/10, operation_type: Merging channels into npy stacks, Time/image: 0.198sec, Time_left: 0.013 min.
+Progress: 7/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.010 min.
+Progress: 8/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.007 min.
+Progress: 9/10, operation_type: Merging channels into npy stacks, Time/image: 0.195sec, Time_left: 0.003 min.
+Progress: 10/10, operation_type: Merging channels into npy stacks, Time/image: 0.196sec, Time_left: 0.000 min.
+plotting 1 images from /home/olafsson/datasets/plate1/test/stack
+Image path:/home/olafsson/datasets/plate1/test/stack/plate1_E02_21_1.npy

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_00_code.txt

@@ -0,0 +1,25 @@
+from spacr.measure import measure_crop
+%matplotlib inline
+
+settings = {'src':'/home/olafsson/datasets/plate1/test/merged', # (path) path to source folder (ens in /merged)
+            'channels':[0,1,2,3],# (list) - list of integers representing available channels
+            'cell_mask_dim':4, # (integer or NoneType) - Cell mask dimension 
+            'cell_min_size':2000, # (integer) - minimum size in px2 of cell objects
+            'nucleus_mask_dim':5, # (integer or NoneType) - Nucleus mask dimension 
+            'nucleus_min_size':1000, # (integer) - minimum size in px2 of nuclei objects
+            'pathogen_mask_dim':6, # (integer or NoneType) - Pathogen mask dimension 
+            'pathogen_min_size':400, # (integer) - minimum size in px2 of pathogen objects
+            'cytoplasm_min_size':0, # (integer) - minimum size in px2 of cutoplasm (cell-(nucleus+pathogen)) objects
+            'save_png':True, # (bool) - save objects as PNGs
+            'crop_mode':['cell'], # (list) - Object(s) to be cropped into images ('cell', 'nuclei', 'pathogen')
+            'use_bounding_box':False, # (bool) - Use bounding box for cropped images instead of object area
+            'png_size':[[224,224]], # (list of lists) - size of single object pngs
+            'normalize':False, # (bool or list) - normalize PNGs to percentiles
+            'png_dims':[0,1,2], # (list) - Dimensions to include in PNG images
+            'normalize_by':'png', # (string) - If normalize, normalize to fov (field of view) or png 
+            'save_measurements':True, # (bool) - Save measurements
+            'plot':True, # (bool) - plot images during analazys
+            'plot_filtration':False, # (bool) - Plot filtration steps
+            'uninfected':False, # (bool) - Include uninfected
+            'test_mode':False, # (bool) - Activate Test mode
+            'test_nr':10} # (integer) - Number of images to analyze in test mode

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_code.txt

@@ -0,0 +1 @@
+measure_crop(settings)

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_00_text.txt

@@ -0,0 +1,3 @@
+Processing folder: /home/olafsson/datasets/plate1/test/merged
+Found path: /home/olafsson/datasets/plate1/test/merged
+Warning reserving 6 CPU cores for other processes, setting n_jobs to 26

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_02_text.txt

@@ -0,0 +1 @@
+Saving settings to /home/olafsson/datasets/plate1/test/settings/measure_crop_settings.csv

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_04_text.txt

@@ -0,0 +1,2 @@
+using 26 cpu cores
+Progress: 0/10, operation_type: Measure and Crop, Time/image: 0.000sec, Time_left: 0.000 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_10_text.txt

@@ -0,0 +1 @@
+Progress: 1/10, operation_type: Measure and Crop, Time/image: 38.097sec, Time_left: 0.220 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_16_text.txt

@@ -0,0 +1 @@
+Progress: 2/10, operation_type: Measure and Crop, Time/image: 43.107sec, Time_left: 0.221 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_22_text.txt

@@ -0,0 +1 @@
+Progress: 3/10, operation_type: Measure and Crop, Time/image: 43.107sec, Time_left: 0.193 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_28_text.txt

@@ -0,0 +1 @@
+Progress: 4/10, operation_type: Measure and Crop, Time/image: 47.621sec, Time_left: 0.183 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_34_text.txt

@@ -0,0 +1 @@
+Progress: 5/10, operation_type: Measure and Crop, Time/image: 59.437sec, Time_left: 0.191 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_40_text.txt

@@ -0,0 +1 @@
+Progress: 6/10, operation_type: Measure and Crop, Time/image: 59.437sec, Time_left: 0.152 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_46_text.txt

@@ -0,0 +1 @@
+Progress: 7/10, operation_type: Measure and Crop, Time/image: 59.437sec, Time_left: 0.114 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_52_text.txt

@@ -0,0 +1 @@
+Progress: 8/10, operation_type: Measure and Crop, Time/image: 59.437sec, Time_left: 0.076 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_58_text.txt

@@ -0,0 +1 @@
+Progress: 9/10, operation_type: Measure and Crop, Time/image: 59.437sec, Time_left: 0.038 min.

spacr-1.0.0/docs/resources/tutorial/2_measure/notebook/2_spacr_generate_mesurments_crop_images-ipynb/cell_01_out_64_text.txt

@@ -0,0 +1,2 @@
+Progress: 10/10, operation_type: Measure and Crop, Time/image: 59.437sec, Time_left: 0.000 min.
+Successfully completed run