Merge branch 'develop' into main

AUTHORS.md

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+## TomoBEAR authors
+
+Max Delbruck Center for Molecular Medicine, Berlin, Germany (<https://www.mdc-berlin.de>)
+
+* Mikhail Kudryashev - project leader
+* Artsemi Yushkevich - developer
+* Vasilii Mikirtumov - application engineer
+
+
+Max Planck Institute of Biophysics, Frankfurt (Hesse), Germany (<https://www.biophys.mpg.de/en>)
+
+* Nikita Balyschew - core version developer
+
+## External modified software authors
+
+TomoBEAR also contains modified pieces of MATLAB source code of the Dynamo package developed by D. Castaño-Díez et al.: https://www.dynamo-em.org.

CHANGELOG.md

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+# Changelog
+
+All notable changes will be documented in this file.
+
+## v0.3.0 - 2023-05-22
+
+### :rocket: New Features
+* ```local_live``` data processing mode - new mode allows to make on-the-fly pre-processing and reconstructions during data collection to check the sample quality. *Currently only single-shot collected data is supported for this feature.*
+* ```EER``` (*Electron Event Representation*) support: input files format perception along with ```.gain``` gain file format support are now enabled in ```MotionCor2``` module
+* ```GenerateParticles``` - new module which allows to generate particles using either Dynamo (by cropping) or SUSAN (by subtomogram reconstructions)
+* ```IsoNet``` - module wrapping [IsoNet](https://github.com/IsoNet-cryoET/IsoNet) - CNN for denoising and missing wedge reconstruction
+
+### :arrow_up: Improvements
+* ```BinStacks```: added possibility to bin non-aligned stacks
+* ```AreTomo```:
+  - enabled binned stack input
+  - enabled local patch-based alignment
+* ```BatchRunTomo```: enabled IMOD-based patch-tracking
+* ```Reconstruct```: enabled [*nonlinear anisotropic diffusion* (NAD)](https://www.sciencedirect.com/science/article/pii/S1047847701944065?via%3Dihub) filter for tomograms post-filtering
+* ```GCTFCtfphaseflipCTFCorrection```: added possibility to use [CTFFIND4](https://www.sciencedirect.com/science/article/pii/S1047847715300460)
+
+### :bug: Major fixes
+* input files perception - fixed duplicated file extension ( issue #16 )
+
+---
+## v0.2.0 - 2023-02-23
+
+### :rocket: New Features
+* `GridEdgeEraser`: a new module which allows to identify position of the grid edge and mask it out.
+  * *Currently only gold grids data is supported for this feature.*
+
+### :arrow_up: Improvements
+* `AreTomo`:
+  * enabled IMOD-compatible files output
+  * enabled tilt axis offset parameter
+
+### :bug: Fixes
+* `EMDTemplateGeneration`: fixed EMDB URL
+* `BatchRunTomo`: fixed bug which prevented running TomoBEAR project for a single tilt serie
+* `GCTFCtfphaseflipCTFCorrection`:
+    * fixed AreTomo-aligned data usage
+    * fixed aligned stack usage
+    * fixed Ctfphaseflip usage
+* `Reconstruct`: fixed reconstruction based on AreTomo-aligned data
+
+---
+## v0.1.2 - 2023-01-20
+
+### :bug: Fixes
+* `AreTomo` module: fixed parallelization and usage

CITATION.cff

@@ -4,7 +4,22 @@ authors:
   - family-names: Balyschew
     given-names: Nikita
     orcid: https://orcid.org/0000-0001-7330-4628
-title: "TomoBEAR: an automated, configurable and customizable full processing pipeline for tomographic cryo electron microscopy data and subtomogram averaging"
-version: 0.1.3.alpha
-doi: 
-date-released: 2021-08-13
+  - family-names: Yushkevich
+    given-names: Artsemi
+    orcid: https://orcid.org/0000-0002-8729-9281
+  - family-names: Mikirtumov
+    given-names: Vasilii
+    orcid:
+  - family-names: Sanchez
+    given-names: Ricardo M.
+    orcid: https://orcid.org/0000-0002-2854-0119
+  - family-names: Sprink
+    given-names: Thiemo
+    orcid: https://orcid.org/0000-0002-0760-6828
+  - family-names: Kudryashev
+    given-names: Misha
+    orcid: https://orcid.org/0000-0003-3550-6274
+title: "Streamlined Structure Determination by Cryo-Electron Tomography and Subtomogram Averaging using TomoBEAR"
+version: 0.3.0
+doi: https://doi.org/10.1101/2023.01.10.523437
+date-released: 2023-05-22