spacr 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- spacr/app_annotate.py +1 -1
- spacr/core.py +1 -0
- spacr/deep_spacr.py +1 -3
- spacr/gui.py +39 -17
- spacr/gui_elements.py +7 -7
- spacr/io.py +14 -4
- spacr/plot.py +57 -0
- spacr/resources/icons/activation.png +0 -0
- spacr/resources/icons/activation_heatmap.png +0 -0
- spacr/resources/icons/logo_spacr.png +0 -0
- spacr/resources/icons/logo_spacr_v1.png +0 -0
- spacr/resources/icons/logo_v1.pdf +2786 -6
- spacr/resources/icons/logo_v2.pdf +274 -0
- spacr/resources/icons/logo_v2_dark.pdf +327 -0
- spacr/resources/icons/logo_v2_dark.png +0 -0
- spacr/resources/icons/logo_v2_white.pdf +386 -0
- spacr/resources/icons/logo_v2_white.png +0 -0
- spacr/settings.py +2 -2
- spacr/spacr_cellpose.py +0 -1
- spacr/utils.py +51 -1
- {spacr-1.0.5.dist-info → spacr-1.0.6.dist-info}/METADATA +1 -1
- {spacr-1.0.5.dist-info → spacr-1.0.6.dist-info}/RECORD +26 -17
- {spacr-1.0.5.dist-info → spacr-1.0.6.dist-info}/entry_points.txt +1 -1
- {spacr-1.0.5.dist-info → spacr-1.0.6.dist-info}/LICENSE +0 -0
- {spacr-1.0.5.dist-info → spacr-1.0.6.dist-info}/WHEEL +0 -0
- {spacr-1.0.5.dist-info → spacr-1.0.6.dist-info}/top_level.txt +0 -0
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trailer
|
Binary file
|
spacr/settings.py
CHANGED
@@ -1022,7 +1022,7 @@ expected_types = {
|
|
1022
1022
|
|
1023
1023
|
categories = {"Paths":[ "src", "grna", "barcodes", "custom_model_path", "dataset","model_path","grna_csv","row_csv","column_csv", "metadata_files", "score_data","count_data"],
|
1024
1024
|
"General": ["cell_mask_dim", "cytoplasm", "cell_chann_dim", "cell_channel", "nucleus_chann_dim", "nucleus_channel", "nucleus_mask_dim", "pathogen_mask_dim", "pathogen_chann_dim", "pathogen_channel", "test_mode", "plot", "metadata_type", "custom_regex", "experiment", "channels", "magnification", "channel_dims", "apply_model_to_dataset", "generate_training_dataset", "train_DL_model", "delete_intermediate", "uninfected", ],
|
1025
|
-
"Cellpose":["
|
1025
|
+
"Cellpose":["fill_in","from_scratch", "n_epochs", "width_height", "model_name", "custom_model", "resample", "rescale", "CP_prob", "flow_threshold", "percentiles", "invert", "diameter", "grayscale", "Signal_to_noise", "resize", "target_height", "target_width"],
|
1026
1026
|
"Cell": ["cell_diamiter","cell_intensity_range", "cell_size_range", "cell_background", "cell_Signal_to_noise", "cell_CP_prob", "cell_FT", "remove_background_cell", "cell_min_size", "cytoplasm_min_size", "adjust_cells", "cells", "cell_loc"],
|
1027
1027
|
"Nucleus": ["nucleus_diamiter","nucleus_intensity_range", "nucleus_size_range", "nucleus_background", "nucleus_Signal_to_noise", "nucleus_CP_prob", "nucleus_FT", "remove_background_nucleus", "nucleus_min_size", "nucleus_loc"],
|
1028
1028
|
"Pathogen": ["pathogen_diamiter","pathogen_intensity_range", "pathogen_size_range", "pathogen_background", "pathogen_Signal_to_noise", "pathogen_CP_prob", "pathogen_FT", "pathogen_model", "remove_background_pathogen", "pathogen_min_size", "pathogens", "pathogen_loc", "pathogen_types", "pathogen_plate_metadata", ],
|
@@ -1039,7 +1039,7 @@ categories = {"Paths":[ "src", "grna", "barcodes", "custom_model_path", "dataset
|
|
1039
1039
|
"Plot": ["split_axis_lims", "x_lim","log_x","log_y", "plot_control", "plot_nr", "examples_to_plot", "normalize_plots", "cmap", "figuresize", "plot_cluster_grids", "img_zoom", "row_limit", "color_by", "plot_images", "smooth_lines", "plot_points", "plot_outlines", "black_background", "plot_by_cluster", "heatmap_feature","grouping","min_max","cmap","save_figure"],
|
1040
1040
|
"Timelapse": ["timelapse", "fps", "timelapse_displacement", "timelapse_memory", "timelapse_frame_limits", "timelapse_remove_transient", "timelapse_mode", "timelapse_objects", "compartments"],
|
1041
1041
|
"Advanced": ["merge_edge_pathogen_cells", "test_images", "random_test", "test_nr", "test", "test_split", "normalize", "target_unique_count","threshold_multiplier", "threshold_method", "min_n","shuffle", "target_intensity_min", "cells_per_well", "nuclei_limit", "pathogen_limit", "background", "backgrounds", "schedule", "test_size","exclude","n_repeats","top_features", "model_type_ml", "model_type","minimum_cell_count","n_estimators","preprocess", "remove_background", "normalize", "lower_percentile", "merge_pathogens", "batch_size", "filter", "save", "masks", "verbose", "randomize", "n_jobs"],
|
1042
|
-
"Beta": ["all_to_mip", "upscale", "upscale_factor", "consolidate", "distance_gaussian_sigma","use_sam_pathogen","use_sam_nucleus", "use_sam_cell"]
|
1042
|
+
"Beta": ["all_to_mip", "upscale", "upscale_factor", "consolidate", "distance_gaussian_sigma","use_sam_pathogen","use_sam_nucleus", "use_sam_cell", "denoise"]
|
1043
1043
|
}
|
1044
1044
|
|
1045
1045
|
|
spacr/spacr_cellpose.py
CHANGED
spacr/utils.py
CHANGED
@@ -1314,7 +1314,7 @@ def _get_cellpose_channels_v2(src, nucleus_channel, pathogen_channel, cell_chann
|
|
1314
1314
|
|
1315
1315
|
return cellpose_channels
|
1316
1316
|
|
1317
|
-
def
|
1317
|
+
def _get_cellpose_channels_v1(src, nucleus_channel, pathogen_channel, cell_channel):
|
1318
1318
|
|
1319
1319
|
cell_mask_path = os.path.join(src, 'masks', 'cell_mask_stack')
|
1320
1320
|
nucleus_mask_path = os.path.join(src, 'masks', 'nucleus_mask_stack')
|
@@ -1346,6 +1346,56 @@ def _get_cellpose_channels(src, nucleus_channel, pathogen_channel, cell_channel)
|
|
1346
1346
|
|
1347
1347
|
return cellpose_channels
|
1348
1348
|
|
1349
|
+
def _get_cellpose_channels(src, nucleus_channel, pathogen_channel, cell_channel):
|
1350
|
+
cell_mask_path = os.path.join(src, 'masks', 'cell_mask_stack')
|
1351
|
+
nucleus_mask_path = os.path.join(src, 'masks', 'nucleus_mask_stack')
|
1352
|
+
pathogen_mask_path = os.path.join(src, 'masks', 'pathogen_mask_stack')
|
1353
|
+
|
1354
|
+
if any(os.path.exists(p) for p in [cell_mask_path, nucleus_mask_path, pathogen_mask_path]):
|
1355
|
+
if any(c is None for c in [nucleus_channel, pathogen_channel, cell_channel]):
|
1356
|
+
print('Warning: Cellpose masks already exist. Unexpected behaviour if any channel is None while masks exist.')
|
1357
|
+
|
1358
|
+
# Enforced order: nucleus → cell → pathogen
|
1359
|
+
logical_order = []
|
1360
|
+
if nucleus_channel is not None:
|
1361
|
+
logical_order.append(('nucleus', nucleus_channel))
|
1362
|
+
if cell_channel is not None:
|
1363
|
+
logical_order.append(('cell', cell_channel))
|
1364
|
+
if pathogen_channel is not None:
|
1365
|
+
logical_order.append(('pathogen', pathogen_channel))
|
1366
|
+
|
1367
|
+
# Remove duplicate values while preserving first occurrence
|
1368
|
+
seen = set()
|
1369
|
+
ordered_channels = []
|
1370
|
+
for name, ch in logical_order:
|
1371
|
+
if ch not in seen:
|
1372
|
+
ordered_channels.append(ch)
|
1373
|
+
seen.add(ch)
|
1374
|
+
|
1375
|
+
# Map actual channel values to capped indices
|
1376
|
+
remap = {ch: min(i, 2) for i, ch in enumerate(ordered_channels)}
|
1377
|
+
|
1378
|
+
# Final channel assignments
|
1379
|
+
cellpose_channels = {}
|
1380
|
+
|
1381
|
+
if nucleus_channel is not None:
|
1382
|
+
c = remap[nucleus_channel]
|
1383
|
+
cellpose_channels['nucleus'] = [c, c]
|
1384
|
+
|
1385
|
+
if cell_channel is not None:
|
1386
|
+
c = remap[cell_channel]
|
1387
|
+
if nucleus_channel is not None:
|
1388
|
+
n = remap[nucleus_channel]
|
1389
|
+
cellpose_channels['cell'] = [n, c]
|
1390
|
+
else:
|
1391
|
+
cellpose_channels['cell'] = [c, c]
|
1392
|
+
|
1393
|
+
if pathogen_channel is not None:
|
1394
|
+
c = remap[pathogen_channel]
|
1395
|
+
cellpose_channels['pathogen'] = [c, c]
|
1396
|
+
|
1397
|
+
return cellpose_channels
|
1398
|
+
|
1349
1399
|
def annotate_conditions(df, cells=None, cell_loc=None, pathogens=None, pathogen_loc=None, treatments=None, treatment_loc=None):
|
1350
1400
|
"""
|
1351
1401
|
Annotates conditions in a DataFrame based on specified criteria and combines them into a 'condition' column.
|