v0.2.0-keep-export

Fix zip name

- .zip.zip tp .zip

v0.2.0

Release notes

• Add XYZ flip operations in data augmentation
• Change MIN_AREA_ELLIPSOID from 20 to 9
• Automatically initialize a new model with the pretrained parameters
• Make detection algorithm compatible with 2D
• Make flow algorithm compatible with 2D
• Make export function compatible with 2D
• Update loss functions for detection (See details in the paper)
• Add tests for GitHub Actions
• Add get_gpus() for getting GPU info from the client software
• Implement upload endpoint for the client software
• Implement dataset endpoint for the client software
• Add environment.yml to reproduce the conda environment
• Implement logger that can be shared with the client software
• Update Colab notebook
• Use averaged training losses in log
• log_interval can be set as a parameter
• Reorganize Redis state management
• Reorganize cancel behavior
• Stop using probability to refine spot radii
• Move keep_axials from model to dataset
• Upgrade tensorflow to 2.4.0
• Organize model reset strategy
  • Versatile -> latest versatile model
  • Default -> self-supervised (detection) or random (flow)
  • URL -> load from the specified URL
• Update README

v0.1.1

Change list

• BugFix: avoid returning empty arrays in ellipsoid

v0.1.0-singularity

This release includes a Singularity definition file based on the ELEPHANT server v0.1.0.

Data

This release is for distributing data (e.g. pretrained model parameters).

ELEPHANT detection model pretrained parameters

• versatile2d.pth: trained with 2D datasets (BF-C2DL-HSC, BF-C2DL-MuSC, DIC-C2DH-HeLa, Fluo-C2DL-MSC, Fluo-N2DH-GOWT1, Fluo-N2DL-HeLa, PhC-C2DH-U373, PhC-C2DL-PSC) from the Cell Tracking Challenge
• versatile3d.pth: trained with 3D datasets (Fluo-C3DH-A549, Fluo-C3DH-H157, Fluo-C3DL-MDA231, Fluo-N3DH-CE, Fluo-N3DH-CHO) from the Cell Tracking Challenge and the PH dataset
• versatile3d_001.pth: same file as versatile3d.pth
• versatile3d_002.pth: trained with 3D datasets (Fluo-C3DH-A549, Fluo-C3DH-H157, Fluo-C3DL-MDA231, Fluo-N3DH-CHO) from the Cell Tracking Challenge and the PH dataset
• versatile3d_003.pth: trained with 3D datasets (Fluo-C3DH-A549, Fluo-C3DH-H157, Fluo-C3DL-MDA231, Fluo-N3DH-CE, Fluo-N3DH-CHO) from the Cell Tracking Challenge
• versatile3d_004.pth: trained with 3D datasets (Fluo-C3DH-A549, Fluo-C3DH-H157, Fluo-N3DH-CE, Fluo-N3DH-CHO) from the Cell Tracking Challenge

ELEPHANT flow model pretrained parameters

• Fluo-N3DH-CE_flow.pth: trained with the CE1 and CE2 datasets
• li13_flow_20201004.pth: trained with the PH dataset

v0.1.0

Fix a version number

version number was wrong