0.4.0

What's Changed

• DynaCLR_V2 Submission by @edyoshikun in #240
• Update README.md to point to NMI 2025 by @mattersoflight in #265
• Update the DLMBL Notebook by @edyoshikun in #278
• Fix deprecated numpy call by @ziw-liu in #281
• Expose Final Z cropping in TripletDataModule by @ziw-liu in #270
• Batched dataloading for contrastive learning by @ziw-liu in #276
• add readthedocs config by @mattersoflight in #289
• Fix preprocessing with zarr-python 3 by @ziw-liu in #294
• Batched transforms by @ziw-liu in #282
• Adding annotation typings by @edyoshikun in #300
• Example for Shearing transform by @edyoshikun in #305
• Patch ModelSummary with BatchTransforms by @edyoshikun in #307
• Remove typo in PC by @edyoshikun in #308
• Strip the slash on fov_name for valid anchors on the triplet by @edyoshikun in #313
• Fix typo in readme by @ziw-liu in #309
• Catch hyperparameter incompatibility in checkpoints by @ziw-liu in #319
• Fix the pseudotrack creation by @edyoshikun in #312
• Zoom map transform by @ziw-liu in #314
• Pin xarray by @ziw-liu in #325
• Use new API from zarr-python 3 by @ziw-liu in #320
• Adding support for pyramids by @edyoshikun in #129
• fix prefetch in cached omezarr data module by @alxndrkalinin in #326
• add 5th and 95th percentile by @ritvikvasan in #317
• 3D ResNet for contrastive learning by @ziw-liu in #285
• Test preprocessing sharded arrays by @ziw-liu in #316
• Write Annotations to AnnData by @srivarra in #303
• Added pre-commit by @srivarra in #330
• Pre-commit on all files by @edyoshikun in #331
• Log the similarity between anchor and negatives by @edyoshikun in #332
• Implementation of Beta VAE for benchmarking by @edyoshikun in #273
• Add precommit to dev dependencies by @alxndrkalinin in #334
• Fix examples by @alxndrkalinin in #336
• Expose loading the ckpt to the contrastive model by @edyoshikun in #340
• Removing duplicate call for random seed for PHATE by @edyoshikun in #341
• Add quickstart for the VCP by @edyoshikun in #343
• VCP Dynaclr Extra updates by @srivarra in #344
• Move and fix annotations for AnnData by @edyoshikun in #347
• compute normalization per timepoint by @ritvikvasan in #345
• Add import statement for FullyConvolutionalMAE in VCP Quickstart by @melissawm in #350
• patching a bug when we added the normalize by time transforms. by @edyoshikun in #360
• cli for linear classifier by @edyoshikun in #355
• Predict volume by @ieivanov in #280
• Test Zarr v2 and v3 for our dataloaders and models by @edyoshikun in #372
• This adds the initial configurable QC metrics by @edyoshikun in #364
• Depend on waveorder>=3.0 by @ieivanov in #395

New Contributors

• @ieivanov made their first contribution in #280

Full Changelog: v0.3.2...v0.4.0