diff --git a/.gitattributes b/.gitattributes index bed0738c7eeb449bca98b5d2f33c89a1ee56349a..f8a68793d77400c9e430e2c2f5aa3e595f73b3ab 100644 --- a/.gitattributes +++ b/.gitattributes @@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text # Video files - compressed *.mp4 filter=lfs diff=lfs merge=lfs -text *.webm filter=lfs diff=lfs merge=lfs -text +measurements.db filter=lfs diff=lfs merge=lfs -text diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..a3ff41a4c5757c49dea97c14ffad1204dd59cc03 --- /dev/null +++ b/README.md @@ -0,0 +1,72 @@ +--- +license: mit +task_categories: + - image-classification +tags: + - spacr + - microscopy + - annotation + - toxoplasma +pretty_name: spaCR Annotate and Classify example data +--- + +# spaCR — Annotate and Classify example data + +Example input for the **Annotate** and **Classify** modules of +[spaCR](https://github.com/EinarOlafsson/spacr). It is the output of a Measure +run, so both modules can be exercised without segmenting or measuring anything +first. + +## What is here + +| Path | What it is | +|---|---| +| `data/` | 2,341 single-cell PNG crops, foldered by phenotype | +| `measurements.db` | The measurements, plus `png_list` and the annotation tables | +| `measurements/active_learning/` | The model card from the first annotation round | +| `settings/annotate_settings.csv` | Settings for the Annotate module | +| `settings/classify_settings.csv` | Settings for the Classify module | + +## It carries real annotations + +`png_list.annotate` holds **88 labels** — 50 of class 1 and 38 of class 2 — +against 2,253 unlabelled crops, with 101 rows of per-round history in +`annotation_rounds`. That is what makes this usable as a *classify* set: a +training example needs labels, and unlabelled crops alone would only exercise +the viewer. + +The first active-learning round is recorded too: 88 labels, 25 held out by +well, `holdout_accuracy` 1.0 on a `StratifiedGroupKFold` split where no well +appears on both sides. Treat that number as a demonstration of the workflow, +not as a result — 88 labels over four wells is a very small set. + +## Paths are RELATIVE, deliberately + +Every path in `measurements.db` and in both settings files is relative to the +dataset root: + +``` +data/single_nucleus/uninfected/plate1_E01/cell_png/plate1_E01_19_1_12.png +``` + +A measurements database normally stores absolute paths, which name the machine +that made it and resolve nowhere else. spaCR's downloader rewrites these to +absolute on arrival, so the database works wherever it is unpacked. If you +unpack it by hand, do the same, or point spaCR at the folder and let it. + +`` in the settings files is a placeholder for the unpack location and +is substituted the same way. + +## Plate layout + +Four wells (E01, E02, L01, L02) from the plate published as +[`einarolafsson/spacr-example-measure`](https://huggingface.co/datasets/einarolafsson/spacr-example-measure), +which holds the merged arrays these crops were cut from. + +## Provenance + +Produced by spaCR's Mask module and then its Measure module, from spaCR's own +example images, with `cpsam` for cells and nuclei and a Toxoplasma-specific +CPSAM checkpoint for pathogens. One field of fifty-two (`plate1_E02_20_1`) +failed to measure — a nucleus label spanning two cells — so the crops come from +51 fields. 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"logistic_regression", + "round": 0 + }, + "settings_hash": "6a5ef58e1b2e21908dc0cb02a1790aa607c0666fcea64948db55ef35803f6352", + "spacr_version": "1.5.0.4", + "split_rule": "split_by=well: held out 1 of 4 well group(s) (25.0%) and 25 of 88 cells (28.4%); requested 25.0%. StratifiedGroupKFold(2) over 4 well groups; no group appears on both sides", + "train_metrics": {}, + "training_set": { + "class_balance": { + "annotated": { + "1": 50, + "2": 38 + } + }, + "imbalance_note": "", + "n_train": 88, + "src": "/home/carruthers/.cache/spacr/example_images/plate1/measurements" + } +} \ No newline at end of file diff --git a/settings/annotate_settings.csv b/settings/annotate_settings.csv new file mode 100644 index 0000000000000000000000000000000000000000..2c3f71e048fc549d37906965d93386c3f4bef08a --- /dev/null +++ b/settings/annotate_settings.csv @@ -0,0 +1,26 @@ +Key,Value +annotation_column,annotate +channels,"r,g,b" +crop_source,png +cv_group_by,well +edge_image,False +edge_thickness,0.1 +edge_transparency,100 +image_size,224 +image_type,cell_png +img_size,200 +measurement, +normalize,False +normalize_channels, +object_size,"(0, 0)" +outline, +outline_sigma,4 +outline_threshold_factor,1.25 +percentiles,"[2, 98]" +queue_by_uncertainty,False +queue_diversity,well +queue_limit,0 +queue_measure,entropy +src,/measurements/measurements.db +threshold, +threshold_direction,higher diff --git a/settings/classify_settings.csv b/settings/classify_settings.csv new file mode 100644 index 0000000000000000000000000000000000000000..c46e436dd09fb87e9e9201cdb014995d8f57c439 --- /dev/null +++ b/settings/classify_settings.csv @@ -0,0 +1,52 @@ +Key,Value +amsgrad,True +annotation_column,annotate +augment,False +batch_size,32 +class_balance,none +class_folder_names,"['nc', 'pc']" +classes,"['1', '2']" +classifier_evaluation,True +crop_source,auto +cross_validation_enabled,False +cross_validation_folds,0 +custom_model_path, +cv_group_by,well +dropout_rate,0.1 +epochs,10 +evaluation_bins,10 +evaluation_calibration,temperature +evaluation_fail_on_leakage,True +gradient_accumulation,True +gradient_accumulation_steps,4 +holdout_plate, +image_size,224 +init_weights,True +intermedeate_save,True +leakage_audit_train_test,True +leakage_hash_content,True +leakage_require_identity,True +learning_rate,0.001 +loss_type,focal_loss +max_failure_rate, +mixed_precision,False +model_type,maxvit_t +n_jobs,30 +nested_cv_inner_folds,0 +normalize,True +optimizer_type,adamw +pin_memory,False +plot,True +resume_checkpoint, +schedule,cosine +src, +strict_errors, +tensorboard,True +test,False +train,True +train_channels,"['r', 'g', 'b']" +train_mode,erm +use_checkpoint,True +val_split,0.1 +verbose,False +weight_decay,1e-05