janni - [Download]

twagner (twagner@undisclosed.example.com) — 2022-07-25T11:19:25+00:00

Just Another Noise 2 Noise Implementation (JANNI) JANNI implements a neural network denoising tool described in NVIDIA's noise2noise paper: Noise2Noise: Learning Image Restoration without Clean Data - arXiv It can be trained on your data without the need of ground truth images. It supports MRC and TIFF format. JANNI can be used a command line tool but also provides an simple interface to integrate into other programs (see

pipeline:window:sxwindow

shaikh (shaikh@undisclosed.example.com) — 2022-05-25T13:47:03+00:00

sp_window Particle Extraction: Window particles from micrographs using the particle coordinates. Usage Usage in command line sp_window.py input_micrograph_pattern input_coordinates_pattern input_ctf_params_source output_directory --selection_list=SELECTION_TEXT_FILE --coordinates_format=FORMAT_NAME --box_size=SIZE --skip_invert --limit_ctf --astigmatism_error=ERROR_THRESHOLD --resample_ratio=RATIO --check_consistency ---filament_width=FILAMENT_WIDTH

pipeline:utilities:sp_center_2d3d - old revision restored (2021/02/18 16:24)

shaikh (shaikh@undisclosed.example.com) — 2022-03-01T15:13:22+00:00

sp_center_2d3d Centering : Utility for centering in 2D or 3D. Usage Usage in command line: sp_center_2d3d.py input_stack_or_volume output_directory --mode=centering_mode --verbosity=verbosity_level --debug --threshsigma=threshold_sigma --applyshift stack_or_volume_to_be_centered --ndilation=number_of_dilations --nerosion=number_of_erosions --volradius=volume_radius --dimensions=number_of_dimensions --stem=output_volume_prefix --threshint=intermediate_threshold --pad=padding_factor

pipeline:subtract:projsubtract

shaikh (shaikh@undisclosed.example.com) — 2021-10-11T17:17:09+00:00

sp_signalsubtract projsubtract Project and Subtract : Compute re-projections of map to be subtracted, and subtract them from the original images. Usage Usage in command line sp_signalsubtract.py projsubtract --origparts=particle_stack --map2subtract=map_to_subtract --projparams=projection_parameters --outdir=output_subtraction_directory --nmontage=number_of_examples --inmem --saveprojs --stats --nonorm --verbosity=verbosity_level

pipeline:subtract:centershift

shaikh (shaikh@undisclosed.example.com) — 2021-10-11T17:15:46+00:00

sp_signalsubtract centershift Center Map : Center map of remaining density. Usage Usage in command line sp_signalsubtract.py centershift --cvol1=map_center_1 --cvol2=map_center_2 --shiftparams=shift_parameters --diffimgs=images_to_subtract --outdir=output_subtraction_directory --volradius=map_radius --apix=pixel_size --verbosity=verbosity_level

pipeline:subtract:sp_mask

shaikh (shaikh@undisclosed.example.com) — 2021-10-11T17:13:32+00:00

sp_signalsubtract sp_mask Generate and Apply Mask : Make a soft mask of the region to be excluded. Usage Usage in command line sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --fullmap=full_map --outdir=output_subtraction_directory --mapthresh=threshold --verbosity=verbosity_level

sphire_1_4 - [Documentation & Tutorial]

mstabrin (mstabrin@undisclosed.example.com) — 2021-07-08T12:01:39+00:00

SPHIRE 1.4 / EMAN 2.9 We are happy to announce the release of SPHIRE 1.4! This release adds GUI support for GPU ISAC and makes SPHIRE fully compatible with TranSPHIRE, allowing you to create on-the-fly reconstructions during data acquisition. As usual, this release is a combined release of SPHIRE, EMAN2, and SPARX. What's new

release_history:stable - [Stable Releases]

mstabrin (mstabrin@undisclosed.example.com) — 2021-05-21T08:02:56+00:00

SPHIRE Stable Release History You will be able to download SPHIRE stable releases here, once we started releasing stable versions. Until then the SPHIRE beta releases are available. Stable Releases * SPHIRE 1.4 * SPHIRE 1.3 * SPHIRE 1.2a * SPHIRE 1.2 * SPHIRE 1.1 * SPHIRE 1.0 Beta Releases *

gpu_isac:gpu_isac_2.3.4.zip - created

fschoenfeld (fschoenfeld@undisclosed.example.com) — 2021-02-22T11:00:24+00:00

pipeline:meridien:smear_cutoff999.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-19T16:53:08+00:00

pipeline:meridien:smear_nocutoff.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-19T16:52:38+00:00

badgef1000.gif - created

twagner (twagner@undisclosed.example.com) — 2021-02-19T09:36:27+00:00

icon_subtract_64.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-02T12:01:59+00:00

pipeline:subtract:centered.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-01T17:20:20+00:00

pipeline:subtract:dofinal.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-01T17:20:19+00:00

pipeline:subtract:testmontage.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-01T17:15:43+00:00

pipeline:subtract:sp_mask.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-01T16:58:31+00:00

pipeline:subtract:4-grouped.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-01T16:53:53+00:00

pipeline:subtract:grouped.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-01T16:53:53+00:00

pipeline:subtract:3-transparent.png - created

shaikh (shaikh@undisclosed.example.com) — 2021-02-01T16:47:22+00:00