Releases scipion-em-xmippTomo

3.24.06 Oceanus

  • New protocols:

    • apply_segmentation: Applies a segmentation to a set of tomograms.

    • segment_morphology: Segments a tomogram by means of thresholding, different kind of filters and morphological operations.

  • Protocols updated

    • deep_misalignment: updated model, minor improvements

    • extract_subtomos: improve extract subtomos readability

  • Protocls fixed

    • dose_filter: Dose filter, removing extract stacks

  • More xmippTomo

    • New xmippBase repository to manage shared protocols with Xmipp

    • protocols deprecated: score_transform, denoising_confidence

    • Removed tilt particles object (not used)

3.23.11 Nereus

  • Protocols updated

    • applyAlignmentTS

    • extract_particlesstacks: Added angles from Tilt Series

    • extract_subtomos: Keeping directions in extract subtomos

    • project_subtomograms: Added angles from Tilt Series

    • deep_misalignment_detection: Update deep misalignment detection with new version of subtomo extraction and fiducial size options

    • subtraction_subtomo: Improved implementation with MPI and md convert

    • cltomo:

    • resolution_local_monotomo: Allowing odd-even associated to the full tomogram

  • Protocls fixed

    • extract_particlestacks: Dose fixes

    • deep_misalignment_detection: Recover deleted methods

    • dose_filter: Dose validation fixed

    • score_coordinates: Test improvements and carbon score fixes

  • More xmippTomo

    • Fixed calculateRotationAngleAndShiftsFromTM

    • Test refactoring

3.23.07 - Morpheus

  • New protocols

    • project_subtomograms (for obtaining sobtomogram projections)

    • extract_particlestacks (extract from tilt series and SetOfTiltSeriesParticle)

    • denoising_confidence

    • extract_particlestacks

    • deep_misalignment_detection (misalignment detection in tomographic reconstructions from high-contrast regions)

    • peak_high_contrast (for detecting high contrast regions in tomographic reconstruction)

  • Protocols updated

    • project_top: Subtomo projector compatible with hdf stacks. Test fixed. Projections keep orientation, Ignore alignments in projection

    • subtomo_map_back, score_coordinates: Mapback scales any reference to match the tomogram sampling

    • subtomo_map_back: Mapback waits now when scheduled and not the reference is needed, works with 3d classes, works with “other tomograms”

    • project_subtomograms: Parallelized protocol

  • More xmipptomo

    • Update requirements.txt

    • Fix tests: protocol_extract_subtomos, monotomo, crop, resize, xmipptomo