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angelolab
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Nimbus
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Add clear documentation to avoid using this repo for predictions
#82
ngreenwald
opened
2 months ago
0
Dimensions are swapped on output
#81
ngreenwald
closed
2 weeks ago
1
Wandb
#80
JLrumberger
closed
6 months ago
2
Adaptation of input images/directory structure for OME.TIFF formatted files.
#79
raymond301
closed
2 weeks ago
4
nimbus.predict_fovs() seems to be hanging indefinitely
#78
whitneyt1
closed
8 months ago
3
Added predict_data_list function to model_builder
#77
JLrumberger
closed
10 months ago
1
Changed unet final layer activation and name
#76
JLrumberger
closed
10 months ago
0
Added dataset and marker filtering
#75
JLrumberger
closed
10 months ago
0
Marker filter
#74
JLrumberger
closed
10 months ago
1
Vanilla unet with valid/same/mirror padding
#73
JLrumberger
closed
10 months ago
1
Cannot find /data/example_dataset/input_data folder in repo
#72
Calebium
closed
10 months ago
1
Added Environment Files
#71
srivarra
opened
11 months ago
2
Add `conda` environment configurations for Linux w/ CUDA and macOS w/ Metal
#70
srivarra
closed
4 months ago
1
Added another path to model checkpoint
#69
JLrumberger
closed
11 months ago
0
Unexplainable "tiling shadows" in prediction masks
#68
svntrx
closed
10 months ago
1
Added code from deepcell repo and changed dependencies in pyproject.toml
#67
JLrumberger
closed
11 months ago
1
Test the model on WSI prediction and streamline inference if necessary
#66
JLrumberger
closed
2 weeks ago
0
Prediction notebook
#65
JLrumberger
closed
1 year ago
2
Clean up application notebooks
#64
ngreenwald
closed
1 year ago
1
Add batch-effects normalization (BEN) training and inference scheme
#63
JLrumberger
closed
2 weeks ago
2
Added BEN scheme sampling for training
#62
JLrumberger
opened
1 year ago
0
Figure out plan for hosting large image datasets
#61
JLrumberger
closed
10 months ago
3
Added seeds to tests and changed conftest to work on my machine
#60
JLrumberger
closed
1 year ago
1
Application notebooks
#59
JLrumberger
closed
1 year ago
1
Coverage Reporting Fix
#58
srivarra
closed
1 year ago
0
Coveralls not reporting
#57
ngreenwald
closed
1 year ago
0
Added mskp and hickey splits
#56
JLrumberger
closed
1 year ago
1
GitHub Actions
#55
srivarra
closed
1 year ago
2
Eval splits
#54
JLrumberger
closed
1 year ago
5
Experiment with pre-processing steps
#53
ngreenwald
closed
10 months ago
6
Added scripts for .tfrecord generation of tonic_annotated and mskcc pancreas datasets.
#52
JLrumberger
closed
1 year ago
0
Fixed evaluation_script argparser and model_builder multi-dataset sampling
#51
JLrumberger
closed
1 year ago
0
Adding more control and train/val/test set composition
#50
JLrumberger
closed
1 year ago
0
Adding more control for validation and test dataset composition
#49
JLrumberger
closed
1 year ago
1
Multi dataset
#48
JLrumberger
closed
1 year ago
15
Added worst n plots and heatmaps of per cell precision, recall, spec, f1
#47
JLrumberger
closed
1 year ago
1
Add nuclei, membrane channel and tissue type attribute to tfrecord dataset generation
#46
JLrumberger
closed
1 year ago
0
Write script for model validation and metric calculation to automatically generate plots and pred cell_table
#45
JLrumberger
closed
1 year ago
0
Dataset processing progress
#44
ngreenwald
opened
1 year ago
0
Include nuclei, membrane channel and tissue_type in dataset generation and training
#43
JLrumberger
closed
1 year ago
0
Added SimpleTFRecords class for handling MSK data
#42
JLrumberger
closed
1 year ago
0
Simple version of SegmentationTFRecords that expects image & label instead of conversion matrix
#41
JLrumberger
closed
1 year ago
0
Meeting notes
#40
JLrumberger
closed
10 months ago
1
Multi dataset training and validation (with additional datasets)
#39
JLrumberger
closed
1 year ago
0
Added resize argument and functionality to SegmentationTFRecords
#38
JLrumberger
closed
1 year ago
0
Added deepcell application wrapper for model
#37
JLrumberger
closed
1 year ago
0
Filter out sparse examples from the training data
#36
JLrumberger
closed
1 year ago
0
Changed the exclude_background_tiles functionality
#35
JLrumberger
closed
1 year ago
0
Filter out sparse examples
#34
JLrumberger
closed
1 year ago
1
Data aug
#33
JLrumberger
closed
1 year ago
1
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