Reverse Dependencies of mrcfile

The following projects have a declared dependency on mrcfile:

• 3dstrudel — Strudel package
• artis — Scientific Methods Software Package
• aspire — Algorithms for Single Particle Reconstruction
• BioTEMPy — TEMPy: a Python Library for Assessment of 3D Electron Microscopy Density Fits
• ccp4ED — Electron diffraction utilities
• ccpem-utils — "Python utils for EM data processing (dev version)"
• cellcanvas — A tool for painting in cellular architecture
• cesped — Code utilities for the CESPED (Cryo-EM Supervised Pose Estimation Dataset) benchmark
• Clement — GUI for Correlative Light and Electron Microscopy
• cryo-qcheck — Quality parameters for cryoEM
• cryoCARE — cryoCARE is a deep learning approach for cryo-TEM tomogram denoising.
• cryoCAT — Contextual Analysis Tools for CryoET
• cryoemservices — Services for CryoEM processing
• cryoet-deepfinder — DeepFinder is an original deep learning approach to localize macromolecules in cryo electron tomography images. The method is based on image segmentation using a 3D convolutional neural network.
• cryohub — IO hub for Cryo-EM, Cryo-ET and subtomogram averaging data.
• cryojax — Cryo-EM image simulation and analysis powered by JAX
• cryosieve — CryoSieve: a particle sorting and sieving algorithm for single particle analysis in cryo-EM
• em-add-scalebar — A package to add a scale bar to microscopy images
• em-mpi-add-scalebar — A package to add a scale bar to microscopy images
• EMalign — EM align
• emda — Electron Microscopy map and model manipulation tools
• emdbva — CryoEM validation toolkit
• emflow — no summary
• empiarreader — EMPIARReader provides utilities to lazily load data from EMPIAR into a machine-learning-friendly dataset format or to locally download the files.
• EmTools — Utilities for CryoEM data manipulation
• fibsem-tools — Tools for processing FIBSEM datasets
• fidder — U-Net for 2D fiducial segmentation in cryo-EM
• galaxy-data — Galaxy datatype framework and datatypes
• GridDataFormats — Reading and writing of data on regular grids in Python
• icebreaker-em — no summary
• impy-array — Speed up coding/extending image analysis in Python.
• instamatic — Python program for automated electron diffraction data collection
• kinlin — WIP: PyTorch based framework
• kltpicker2 — KLT Picker: Particle picking using data-driven optimal templates
• lil-aretomo — AreTomo (w)rapper for rln4
• liver-ct-segmentation-package — Prediction package for U-Net models trained on the LiTS dataset.
• localres — Plot the histogram of local resolution values of a cryo-EM reconstruction
• logdensity — take the logarithm of a cryo-EM density
• magCalEM — A program to calibrate the pixel size of cryoEM data
• MagCalibration-jdickerson80 — A program to calibrate the pixel size of cryoEM data
• maptools — Manipulate maps
• MDCatch — Fetch metadata from EPU / SerialEM and launch on-the-fly pre-processing
• mdml — Application of Deep learning on molecular dymanamics trajectories
• membrain-seg — membrane segmentation in 3D for cryo-ET
• miffi — cryo-EM micrograph filtering utilizing Fourier space information
• mrchead — CLI tool for viewing mrc file headers
• mrcsmooth — Downsample cryo-EM densities
• naaf — IO hub for Cryo-EM, Cryo-ET and subtomogram averaging data.
• napari-boxmanager — Particle selection tool for cryo-em
• napari-deepfinder — A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.
• napari-mrcfile-handler — A simple plugin to read, write and adjust mrcfiles in napari.
• napari-mrcfile-reader — Read MRC2014 files in napari using mrcfile.
• napari-subboxer — A napari plugin for interacting with electron cryotomograms
• napari-tomoslice — A napari plugin for interacting with electron cryotomograms
• occupy — OccuPy: Estimation of local scale in cryo-EM maps
• ot2rec-report — Generate reports for Ot2Rec
• peepingtom — Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
• perfectem — Run TEM performance tests with SerialEM
• pycistem — Python tools to run cisTEM programs and code
• pyserialem — Python module to read/write SerialEM .nav files.
• pytom-match-pick — PyTOM's GPU template matching module as an independent package
• quoll — Image quality assessment for electron tomography
• relion — Relion Python API
• reliontomotools — Additional tools for Relion tomo
• ridge-detection — ridge / line detection algorithm
• rigidbodyfit — Align biomolecular structures with densities
• roodmus — Synthetic SP micrograph creation and analysis
• scipion-em — This modules contains classes related with EM
• scipion-em-continuousflex — Plugin to use continuousflex protocols within the Scipion framework
• scipion-em-kiharalab — Scipion plugin in order to use ther kiharalab software
• scipion-em-tomo — Plugin to use electron tomography software within the Scipion framework
• scipion-em-tomosegmemtv — Scipion plugin for softare packages tomosegmemTV and membraneAnnotator.
• scipion-em-ucm — Scipion plugin with map validations
• scipion-em-warp — Plugin to use Warp within the Scipion framework
• sfftk — Toolkit for working with EMDB-SFF and other segmentation file formats
• simplectf — Setting up a python package
• SimpliPyTEM — A python package to simplify the processing and analysis of TEM and in situ TEM images and videos
• smartem — Tool to trace cryoEM SPA processing results through the magnification hierarchy provided by EPU
• starstack — A relion star mrcs stack class
• stemia — A personal collection of (sometimes...) useful scripts and tools for cryoem/cryoet.
• StitchM — A package for stitching mosaics from Cockpit with (or without) ROIs
• struvolpy — "A python package for parsing atomic coordinates files and electron density maps"
• surforama — a tool for using surfaces to explore volumetric data in napari
• test-em-add-scalebar — A package to add a scale bar to microscopy images
• threed-strudel — Strudel package
• tiltstack — stack tilt images into tilt-series, keeping track of metadata
• tomogram-shift-alignment — Program to compare the shifts between two of the same tomogram which were constructed by different TSA methods, and to adjust the particle coordinates of a star file to fit the new tomogram.
• tomotwin-cryoet — Picking procedure for cryo em tomography
• transphire — Automated post data aquisition processing tool
• transphire-transform — Utilites to change between SPHIRE, RELION and to modify the data
• VA — CryoEM validation toolkit
• xmipp-metadata — Package to handle Xmipp Metadata and image binary data
• yet-another-imod-wrapper — A simple API for automated tilt-series alignment using IMOD