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CHANGES.txt
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Dec 19, 2024 - **v4.2.0**
Compatibility with cryoSPARC v4.6.2
Adding 3D Flex Generator Protocol
Generating the particles and the consensus volume in the 3D Flex Data Prepare protocol
Validating the mask in the 3d Flex Mesh protocol
Showing CS logs
Nov 13, 2024 - **v4.1.6**
Fix parameter mask help as described in https://github.com/scipion-em/scipion-em-cryosparc2/issues/170
Oct 10, 2024 - **v4.1.5**
Compatibility with cryoSPARC v4.6
Aug 28, 2024 - **v4.1.4**
Compatibility with cryoSPARC v4.5.3
May 19, 2024 - **v4.1.2**
fixed: Installation Hot fix
May 17, 2024 - **v4.1.1**
Compatibility with cryoSPARC v4.5.1
Registering flex particles
Integration with FlexUtils plugin
April 25, 2024 - **v4.1.0**
Tolerating deletion of projects within CS as well as their folders in the file system
Add new protocols:
* **3D Flex Data Prep**: Prepares particles for use in 3DFlex training and reconstruction. At the same way, Takes in a consensus (rigid) refinement density map, plus optionally a segmentation and generates a tetrahedral mesh for 3DFlex.
* **3D Flex Mesh Prep**: Takes in a consensus (rigid) refinement density map, plus optionally a segmentation and generates a tetrahedral mesh for 3DFlex. See Mesh Generation below.
* **3D Flex Training**: Uses a mesh and prepared particles (at a downsampled resolution) to train a 3DFlex model. Parameters control the number of latent dimensions, size of the model, and training hyperparameters. This job outputs checkpoints during training.
* **3D Flex Reconstruction**: Takes in a checkpoint from training as well as prepared high-resolution particles and performs high-resolution refinement using L-BFGS under the 3DFlex model. This is the stage at which improvements to density in high-res regions are computed. Outputs two half-maps that can be used for FSC validation, sharpening, and other downstream tasks.
Allowing Scipion to import coordinates
April 2, 2024 - **v4.0.11**
Compatibility with cryoSPARC v4.4.1 + Patch
Dec 22, 2023 - **v4.0.10**
Compatibility with cryoSPARC v4.4.1
Add new protocols:
* **3D Variability Analysis**: Protocol to compute the principle modes of variability with a dataset of aligned particles
* **3D Variability Display**: Protocol to create various versions of a 3D variability result that can be used for display
* **Blob Picker**: Automatically picks particles by searching for Gaussian signals.
* **Patch CTF Estimation**: Patch-based CTF estimation automatically estimates defocus variation for tilted, bent, deformed samples and is accurate for all particle sizes and types including flexible and membrane proteins.
Nov 17, 2023 - **v4.0.9**
Compatibility with cryoSPARC v4.4.0
Handling aborted protocols/jobs
June 24, 2023 - **v4.0.8**
Compatibility with cryoSPARC v4.3.1
Deprecated protocols removed: Legacy Refine, Legacy no uniform refine, Legacy naive local refine.
Symmetry moved to unit cell in refinements' output
Generation of star files using relion cancelled (not robust in all cases).
June 1, 2023 - **v4.0.7**
Fixed an error related with the shifts(shifts were not being calculated)
Checking the shifts in a test
Taking the rlnOriginXAngst, rlnOriginYAngst and rlnOriginZAngst
values from .star file generated by pyem library and using them to
calculate the particles shifts
May 26, 2023 - **v4.0.6**
Compatibility with cryoSPARC v4.2.1
Plugin operation in a cluster
Fixed an installation error
May 26, 2023 - **v4.0.5**
Plugin operation in a cluster
Fixed an installation error
March 16, 2023 - **v4.0.4**
Compatibility with cryoSPARC v4.2.1
March 1, 2023 - **v4.0.3**
Compatibility with cryoSPARC v4.2
Fixed an error importing volumes with halves
Fixed an error launching the protocols viewers
Jan 24, 2023 - **v4.0.2**
Compatibility with v4.1.2 CS version
Creating an environment for pyem package
3D homogeneous refinement(Legacy), 3D non-uniform refinement(Legacy) and Naive local refinement(Legacy) protocols are deprecated
Jan 18, 2023 - - Compatibility with v4.1.1 CS version
**v4.0.1**
Nov 8, 2022 - - Compatibility with v4.0.x CS version
**v4.0.0**
Oct 25, 2022 - Hot fixes
**v3.3.19**
* **fixed** : Fixed an error related to Phase Randomized Masket Map calculation
Sept 7, 2022 - Adding functionalities (v3.3.18)
**v3.3.18**
-----------
* **new** * : Allow to import .cs particles files
Sept 1, 2022 - Fixing errors (v3.3.17)
**v3.3.17**
-----------
* **fixed** : Allow 31 or more classes in the 3D classification protocol
Jun 23, 2022 - Fixing errors (v3.3.16)
**v3.3.16**
-----------
* **fixed** : Fixed an error related with the slow loading protocols
* **fixed** : Fixed an error in the 3D classification protocol
Jun 15, 2022 - Compatibility with v3.3.3 CS version (v3.3.15)
Jun 10, 2022 - Redefining CS commands in order to launch the protocols in a cluster
**v3.3.14**
----------
* **new** : Added the option to use the plugin in a CS installation in a cluster
* **new** : Added a wizard to select the lane where the protocols will be launched
* **new** : Added the varaiable CRYOSPARC_DEFAULT_LANE to define the name of the cryoSPARC default lane
* **new** : Added the variable CRYOSPARC_STANDALONE_INSTALLATION to specify whether the CS installation is standalone or not
Jan 18, 2022 - Using emtable library to read star files(improving the performance when generating the outputs)
Nov 12, 2021 - Adding homogenous reconstruction protocol
Feb 11, 2021 - Compatibility with v3.X.X CS versions Adding a new protocol(helical refinement)
Dec 18, 2020 - Cleaning intermediates results
Dec 14, 2020 - Fixing some bugs taking the las iteration in the 2D classification
Apr 10, 2020 - Create a protocol base, Clean the code
Apr 4, 2020 - Add the use of multiple GPUs
Dec 9, 2019 - Migrated to python3
May 27, 2019 - Initial plugin version