.. _gallery: Gallery ======================================== Spring3d -------- :ref:`segmentrefine3d` ^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: sr3d_parameters +--------------------------------------------------+--------------------------------------------------+ | |segmentrefine3d_input.png| | |segmentrefine3d_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Image input stack refinement | Output: Output volume name | +--------------------------------------------------+--------------------------------------------------+ .. |segmentrefine3d_input.png| image:: ../gallery_images/segmentrefine3d_input.png :alt: tree :width: 4 cm :target: ../_images/segmentrefine3d_input.png .. |segmentrefine3d_output.png| image:: ../gallery_images/segmentrefine3d_output.png :alt: tree :width: 4 cm :target: ../_images/segmentrefine3d_output.png :ref:`segrefine3dinspect` ^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: segrefine3dinspect +--------------------------------------------------+--------------------------------------------------+ | |segrefine3dinspect_input.png| | |segrefine3dinspect_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Volume reconstruction | Output: Interactive screenshot | +--------------------------------------------------+--------------------------------------------------+ .. |segrefine3dinspect_input.png| image:: ../gallery_images/segrefine3dinspect_input.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dinspect_input.png .. |segrefine3dinspect_output.png| image:: ../gallery_images/segrefine3dinspect_output.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dinspect_output.png :ref:`segrefine3dgrid` ^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: segrefine3dgrid +--------------------------------------------------+--------------------------------------------------+ | |segrefine3dgrid_input.png| | |segrefine3dgrid_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Image input stack refinement | Output: Output volume name | +--------------------------------------------------+--------------------------------------------------+ .. |segrefine3dgrid_input.png| image:: ../gallery_images/segrefine3dgrid_input.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dgrid_input.png .. |segrefine3dgrid_output.png| image:: ../gallery_images/segrefine3dgrid_output.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dgrid_output.png :ref:`seggridexplore` ^^^^^^^^^^^^^^^^^^^^^ .. automodule:: seggridexplore +--------------------------------------------------+--------------------------------------------------+ | |segrefine3dgrid_output.png| | |seggridexplore_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Grid database | Output: Subgrid merge option | +--------------------------------------------------+--------------------------------------------------+ .. |segrefine3dgrid_output.png| image:: ../gallery_images/segrefine3dgrid_output.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dgrid_output.png .. |seggridexplore_output.png| image:: ../gallery_images/seggridexplore_output.png :alt: tree :width: 4 cm :target: ../_images/seggridexplore_output.png :ref:`segmultirefine3d` ^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: segmultirefine3d +--------------------------------------------------+--------------------------------------------------+ | |segmultirefine3d_input.png| | |segmultirefine3d_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Image input stack refinement | Output: Output volume name | +--------------------------------------------------+--------------------------------------------------+ .. |segmultirefine3d_input.png| image:: ../gallery_images/segmultirefine3d_input.png :alt: tree :width: 4 cm :target: ../_images/segmultirefine3d_input.png .. |segmultirefine3d_output.png| image:: ../gallery_images/segmultirefine3d_output.png :alt: tree :width: 4 cm :target: ../_images/segmultirefine3d_output.png :ref:`segclassreconstruct` ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: segclassreconstruct_prep +--------------------------------------------------+--------------------------------------------------+ | |segclassreconstruct_input.png| | |segclassreconstruct_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Class average stack | Output: Volume name | +--------------------------------------------------+--------------------------------------------------+ .. |segclassreconstruct_input.png| image:: ../gallery_images/segclassreconstruct_input.png :alt: tree :width: 4 cm :target: ../_images/segclassreconstruct_input.png .. |segclassreconstruct_output.png| image:: ../gallery_images/segclassreconstruct_output.png :alt: tree :width: 4 cm :target: ../_images/segclassreconstruct_output.png :ref:`segrefine3dplot` ^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: segrefine3dplot +--------------------------------------------------+--------------------------------------------------+ | |segclassreconstruct_output.png| | |segrefine3dplot_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: refinement.db file | Output: Interactive screenshot | +--------------------------------------------------+--------------------------------------------------+ .. |segclassreconstruct_output.png| image:: ../gallery_images/segclassreconstruct_output.png :alt: tree :width: 4 cm :target: ../_images/segclassreconstruct_output.png .. |segrefine3dplot_output.png| image:: ../gallery_images/segrefine3dplot_output.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dplot_output.png :ref:`segrefine3dcyclexplore` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: segrefine3dcyclexplore +--------------------------------------------------+--------------------------------------------------+ | |segrefine3dplot_output.png| | |segrefine3dcyclexplore_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: refinement.db file | Output: Interactive screenshot | +--------------------------------------------------+--------------------------------------------------+ .. |segrefine3dplot_output.png| image:: ../gallery_images/segrefine3dplot_output.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dplot_output.png .. |segrefine3dcyclexplore_output.png| image:: ../gallery_images/segrefine3dcyclexplore_output.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dcyclexplore_output.png :ref:`segclassmodel` ^^^^^^^^^^^^^^^^^^^^ .. automodule:: segclassmodel +--------------------------------------------------+--------------------------------------------------+ | |segclassmodel_input.png| | |segclassmodel_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Reference volumes | Output: Class average stack | +--------------------------------------------------+--------------------------------------------------+ .. |segclassmodel_input.png| image:: ../gallery_images/segclassmodel_input.png :alt: tree :width: 4 cm :target: ../_images/segclassmodel_input.png .. |segclassmodel_output.png| image:: ../gallery_images/segclassmodel_output.png :alt: tree :width: 4 cm :target: ../_images/segclassmodel_output.png Spring2d -------- :ref:`segment` ^^^^^^^^^^^^^^ .. automodule:: segment_prep +--------------------------------------------------+--------------------------------------------------+ | |segment_input.png| | |segment_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrographs | Output: Image output stack | +--------------------------------------------------+--------------------------------------------------+ .. |segment_input.png| image:: ../gallery_images/segment_input.png :alt: tree :width: 4 cm :target: ../_images/segment_input.png .. |segment_output.png| image:: ../gallery_images/segment_output.png :alt: tree :width: 4 cm :target: ../_images/segment_output.png :ref:`segmentexam` ^^^^^^^^^^^^^^^^^^ .. automodule:: segmentexam +--------------------------------------------------+--------------------------------------------------+ | |segmentexam_input.png| | |segmentexam_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Image input stack | Output: Diagnostic plot | +--------------------------------------------------+--------------------------------------------------+ .. |segmentexam_input.png| image:: ../gallery_images/segmentexam_input.png :alt: tree :width: 4 cm :target: ../_images/segmentexam_input.png .. |segmentexam_output.png| image:: ../gallery_images/segmentexam_output.png :alt: tree :width: 4 cm :target: ../_images/segmentexam_output.png :ref:`segmentclass` ^^^^^^^^^^^^^^^^^^^ .. automodule:: segmentclass +--------------------------------------------------+--------------------------------------------------+ | |segmentclass_input.png| | |segmentclass_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Image input stack | Output: Class average stack | +--------------------------------------------------+--------------------------------------------------+ .. |segmentclass_input.png| image:: ../gallery_images/segmentclass_input.png :alt: tree :width: 4 cm :target: ../_images/segmentclass_input.png .. |segmentclass_output.png| image:: ../gallery_images/segmentclass_output.png :alt: tree :width: 4 cm :target: ../_images/segmentclass_output.png :ref:`segmentalign2d` ^^^^^^^^^^^^^^^^^^^^^ .. automodule:: segmentalign2d_prep +--------------------------------------------------+--------------------------------------------------+ | |segmentalign2d_input.png| | |segmentalign2d_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Image input stack | Output: Image output stack | +--------------------------------------------------+--------------------------------------------------+ .. |segmentalign2d_input.png| image:: ../gallery_images/segmentalign2d_input.png :alt: tree :width: 4 cm :target: ../_images/segmentalign2d_input.png .. |segmentalign2d_output.png| image:: ../gallery_images/segmentalign2d_output.png :alt: tree :width: 4 cm :target: ../_images/segmentalign2d_output.png :ref:`segclassexam` ^^^^^^^^^^^^^^^^^^^ .. automodule:: segclassexam +--------------------------------------------------+--------------------------------------------------+ | |segclassexam_input.png| | |segclassexam_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Class average stack | Output: Diagnostic plot | +--------------------------------------------------+--------------------------------------------------+ .. |segclassexam_input.png| image:: ../gallery_images/segclassexam_input.png :alt: tree :width: 4 cm :target: ../_images/segclassexam_input.png .. |segclassexam_output.png| image:: ../gallery_images/segclassexam_output.png :alt: tree :width: 4 cm :target: ../_images/segclassexam_output.png :ref:`segclasslayer` ^^^^^^^^^^^^^^^^^^^^ .. automodule:: segclasslayer +--------------------------------------------------+--------------------------------------------------+ | |segclasslayer_input.png| | |segclasslayer_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Class average stack | Output: Interactive screenshot | +--------------------------------------------------+--------------------------------------------------+ .. |segclasslayer_input.png| image:: ../gallery_images/segclasslayer_input.png :alt: tree :width: 4 cm :target: ../_images/segclasslayer_input.png .. |segclasslayer_output.png| image:: ../gallery_images/segclasslayer_output.png :alt: tree :width: 4 cm :target: ../_images/segclasslayer_output.png :ref:`seglayer2lattice` ^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: seglayer2lattice +--------------------------------------------------+--------------------------------------------------+ | |seglayer2lattice_input.png| | |seglayer2lattice_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Analyze power spectrum | Output: Power spectrum input image | +--------------------------------------------------+--------------------------------------------------+ .. |seglayer2lattice_input.png| image:: ../gallery_images/seglayer2lattice_input.png :alt: tree :width: 4 cm :target: ../_images/seglayer2lattice_input.png .. |seglayer2lattice_output.png| image:: ../gallery_images/seglayer2lattice_output.png :alt: tree :width: 4 cm :target: ../_images/seglayer2lattice_output.png :ref:`segmentplot` ^^^^^^^^^^^^^^^^^^ .. automodule:: segmentplot +--------------------------------------------------+--------------------------------------------------+ | |seglayer2lattice_output.png| | |segmentplot_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: spring.db file | Output: Interactive screenshot | +--------------------------------------------------+--------------------------------------------------+ .. |seglayer2lattice_output.png| image:: ../gallery_images/seglayer2lattice_output.png :alt: tree :width: 4 cm :target: ../_images/seglayer2lattice_output.png .. |segmentplot_output.png| image:: ../gallery_images/segmentplot_output.png :alt: tree :width: 4 cm :target: ../_images/segmentplot_output.png Springmicrograph ---------------- :ref:`scansplit` ^^^^^^^^^^^^^^^^ .. automodule:: scansplit +--------------------------------------------------+--------------------------------------------------+ | |scansplit_input.png| | |scansplit_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrographs | Output: Output micrograph pattern | +--------------------------------------------------+--------------------------------------------------+ .. |scansplit_input.png| image:: ../gallery_images/scansplit_input.png :alt: tree :width: 4 cm :target: ../_images/scansplit_input.png .. |scansplit_output.png| image:: ../gallery_images/scansplit_output.png :alt: tree :width: 4 cm :target: ../_images/scansplit_output.png :ref:`micexam` ^^^^^^^^^^^^^^ .. automodule:: micexam +--------------------------------------------------+--------------------------------------------------+ | |micexam_input.png| | |micexam_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrographs | Output: Diagnostic plot pattern | +--------------------------------------------------+--------------------------------------------------+ .. |micexam_input.png| image:: ../gallery_images/micexam_input.png :alt: tree :width: 4 cm :target: ../_images/micexam_input.png .. |micexam_output.png| image:: ../gallery_images/micexam_output.png :alt: tree :width: 4 cm :target: ../_images/micexam_output.png :ref:`michelixtrace` ^^^^^^^^^^^^^^^^^^^^ .. automodule:: michelixtrace +--------------------------------------------------+--------------------------------------------------+ | |michelixtrace_input.png| | |michelixtrace_output.pdf| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrographs | Output: Diagnostic plot pattern | +--------------------------------------------------+--------------------------------------------------+ .. |michelixtrace_input.png| image:: ../gallery_images/michelixtrace_input.png :alt: tree :width: 4 cm :target: ../_images/michelixtrace_input.png .. |michelixtrace_output.pdf| image:: ../gallery_images/michelixtrace_output.pdf :alt: tree :width: 4 cm :target: ../_images/michelixtrace_output.pdf :ref:`michelixtracegrid` ^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: michelixtrace +--------------------------------------------------+--------------------------------------------------+ | |michelixtracegrid_input.png| | |michelixtracegrid_output.pdf| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrographs | Output: Diagnostic plot pattern | +--------------------------------------------------+--------------------------------------------------+ .. |michelixtracegrid_input.png| image:: ../gallery_images/michelixtracegrid_input.png :alt: tree :width: 4 cm :target: ../_images/michelixtracegrid_input.png .. |michelixtracegrid_output.pdf| image:: ../gallery_images/michelixtracegrid_output.pdf :alt: tree :width: 4 cm :target: ../_images/michelixtracegrid_output.pdf :ref:`micctfdetermine` ^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: micctfdetermine +--------------------------------------------------+--------------------------------------------------+ | |micctfdetermine_input.png| | |micctfdetermine_output.pdf| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrographs | Output: Diagnostic plot pattern | +--------------------------------------------------+--------------------------------------------------+ .. |micctfdetermine_input.png| image:: ../gallery_images/micctfdetermine_input.png :alt: tree :width: 4 cm :target: ../_images/micctfdetermine_input.png .. |micctfdetermine_output.pdf| image:: ../gallery_images/micctfdetermine_output.pdf :alt: tree :width: 4 cm :target: ../_images/micctfdetermine_output.pdf :ref:`scanrowcolcorr` ^^^^^^^^^^^^^^^^^^^^^ .. automodule:: scanrowcolcorr +--------------------------------------------------+--------------------------------------------------+ | |scanrowcolcorr_input.png| | |scanrowcolcorr_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrograph | Output: Diagnostic plot | +--------------------------------------------------+--------------------------------------------------+ .. |scanrowcolcorr_input.png| image:: ../gallery_images/scanrowcolcorr_input.png :alt: tree :width: 4 cm :target: ../_images/scanrowcolcorr_input.png .. |scanrowcolcorr_output.png| image:: ../gallery_images/scanrowcolcorr_output.png :alt: tree :width: 4 cm :target: ../_images/scanrowcolcorr_output.png :ref:`scandotfit` ^^^^^^^^^^^^^^^^^ .. automodule:: scandotfit +--------------------------------------------------+--------------------------------------------------+ | |scandotfit_input.png| | |scandotfit_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrograph | Output: Diagnostic plot | +--------------------------------------------------+--------------------------------------------------+ .. |scandotfit_input.png| image:: ../gallery_images/scandotfit_input.png :alt: tree :width: 4 cm :target: ../_images/scandotfit_input.png .. |scandotfit_output.png| image:: ../gallery_images/scandotfit_output.png :alt: tree :width: 4 cm :target: ../_images/scandotfit_output.png :ref:`scanlinefit` ^^^^^^^^^^^^^^^^^^ .. automodule:: scanlinefit +--------------------------------------------------+--------------------------------------------------+ | |scanlinefit_input.png| | |scanlinefit_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrograph | Output: Diagnostic plot | +--------------------------------------------------+--------------------------------------------------+ .. |scanlinefit_input.png| image:: ../gallery_images/scanlinefit_input.png :alt: tree :width: 4 cm :target: ../_images/scanlinefit_input.png .. |scanlinefit_output.png| image:: ../gallery_images/scanlinefit_output.png :alt: tree :width: 4 cm :target: ../_images/scanlinefit_output.png