cima package
Chromatin Imaging Analysis (CIMA) is a Python package designed to facilitate the automated detection, assessment, and analysis of complex chromatin tracing experiments
Authors: Ivan Piacere, Iago Meceda Porto, Anthony Palmieri, Mattia Roccatello, Irene Farabella
### Installation
[CIMA installation](https://gitlab.iit.it/ina/CIMA/-/blob/main/Notebooks/Installing%20CIMA.ipynb?ref_type=heads)
### CIMA demo notebooks
[Notebooks](https://gitlab.iit.it/ina/CIMA/-/tree/main/Notebooks?ref_type=heads)
Guided identification of Volumetric CT
QC Assessment
Morphological and Spatial quantification
Volumetric CT comparison with HiC
Ball and Stick CT comparison with HiC
### CIMA tools
CIMA also provides a set of command-line tools installed with the library, supporting both quality assessment and chromatin segment comparison. Each tool is accompanied by comprehensive help text to guide users, including those without advanced technical expertise.
[CIMA tools](https://gitlab.iit.it/ina/CIMA/-/tree/main/CIMATools)
implemeted by Iago Maceda Porto
### CIMA API Documentation
NOTE: After the publication, CIMA will be public to all the users and the API will have a dedicated page. In the meantime, you can browse it off-line from:
[CIMA API](https://gitlab.iit.it/ina/CIMA/-/tree/main/pdocCIMA)
### Citation
If you use CIMA, please cite:<br>
Nir* G, Farabella* I, Pérez Estrada* C, Ebeling* CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet. 2018 Dec 26;14(12):e1007872. doi: 10.1371/journal.pgen.1007872. PMID: 30586358; PMCID: PMC6324821.
Other specific references:<br> Farabella et al (2015) TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits. J. Appl. Cryst. 48, 1314-1323
### FAQ
If you have any question remaining, we would be happy to answer informally: irene.farabella@iit.it
Subpackages
- cima.assessment package
- cima.detection package
- Submodules
- cima.detection.beads_identification module
- cima.detection.clusters module
DBscan()DBscan_grid_search_stableHDBSCAN_stableHDBSCAN_stable.ari_medianHDBSCAN_stable.ari_varHDBSCAN_stable.all_labelsHDBSCAN_stable.min_cluster_size_rangeHDBSCAN_stable.segmentHDBSCAN_stable.ordered_params_dfHDBSCAN_stable.best_mcsHDBSCAN_stable.best_indHDBSCAN_stable.labels_HDBSCAN_stable.optimal_segmentHDBSCAN_stable.copy()HDBSCAN_stable.fit()HDBSCAN_stable.mergeOtherHDBSCANGrid()HDBSCAN_stable.plotAriGrid()HDBSCAN_stable.plotAriVarGrid()HDBSCAN_stable.saveLog()
ThresholdClusterFilterThresholdClusterFilter.features_to_useThresholdClusterFilter.feats_dfThresholdClusterFilter.limitsThresholdClusterFilter.where_retainThresholdClusterFilter.retained_clusters_idsThresholdClusterFilter.transformed_segmentThresholdClusterFilter.new_labelsThresholdClusterFilter.fit()ThresholdClusterFilter.plot()ThresholdClusterFilter.writeMRCs()
getPointwiseDensity()search_epsilon()
- cima.maps package
- Submodules
- cima.maps.density_properties module
- cima.maps.emmap module
MapMap.box_size()Map.centre()Map.change_origin()Map.copy()Map.downsample_map()Map.fourier_transform()Map.getBinaryMap()Map.getFilledMap()Map.getMap()Map.get_com()Map.get_line_between_points()Map.get_normal_vector()Map.get_point_map()Map.get_pos()Map.get_primary_boundary()Map.get_second_boundary()Map.get_significant_points()Map.get_vectors()Map.header_to_binary()Map.laplace_filtered()Map.makeKDTree()Map.make_bin_map()Map.map_rotate_by_axis_angle()Map.map_size()Map.matrix_transform()Map.max()Map.mean()Map.median()Map.min()Map.normalise()Map.origin_change_maps()Map.pad_map()Map.pixel_centre()Map.resample_by_apix()Map.resample_by_box_size()Map.resize_map()Map.rotate_by_axis_angle()Map.rotate_by_euler()Map.rotate_by_matrix()Map.scale_map()Map.shift_origin()Map.std()Map.threshold_map()Map.translate()Map.update_header()Map.vectorise_point()Map.write_to_MRC_file()Map.x_origin()Map.x_size()Map.y_origin()Map.y_size()Map.z_origin()Map.z_size()
- cima.maps.map_features module
GetArea_abovecontour()GetArea_equivalent_diameter()GetEccenticity_abovecontour()GetEllipticity_abovecontour()GetSparseness()GetSphericity()GetSphericity_bribiesca()GetVolume_abovecontour()GetVolume_equivalent_diameter()getClassicalCompactness()getConvexHullVolume()getConvexMap()getConvexity()getDiscreteCompactness()getHolelessSolidity()getMapRelativePointsFromMap()getPointsFromMap()getSolidity()
- cima.maps.map_parser module
- cima.maps.map_spatial_features module
- cima.maps.maptomap module
- cima.maps.scoring_functions module
ScoringFunctionsScoringFunctions.CCC_map()ScoringFunctions.FSC_betweenMaps()ScoringFunctions.LSF()ScoringFunctions.MI()ScoringFunctions.envelope_score()ScoringFunctions.envelope_score_map()ScoringFunctions.getMapsOverlap()ScoringFunctions.get_partial_DLSF()ScoringFunctions.laplace_CCC()ScoringFunctions.normal_vector_score()
- cima.maps.structure_blurrer module
StructureBlurrerStructureBlurrer.gaussian_blur()StructureBlurrer.gaussian_blur_box()StructureBlurrer.gaussian_blur_real_space()StructureBlurrer.gaussian_blur_real_space_box()StructureBlurrer.get_coordinates()StructureBlurrer.get_indices()StructureBlurrer.hard_sphere()StructureBlurrer.hard_sphere_box()StructureBlurrer.make_atom_overlay_map()StructureBlurrer.make_atom_overlay_map1()StructureBlurrer.make_atom_overlay_mapB()StructureBlurrer.mapGridPosition()StructureBlurrer.mapGridPositions()StructureBlurrer.mapGridPositions_vdw()StructureBlurrer.maptree()StructureBlurrer.model_tree()StructureBlurrer.protMap()StructureBlurrer.protMapBox()
- cima.maps.vq module
- cima.parsers package
- cima.patches package
- cima.segments package
- Submodules
- cima.segments.segment_convex module
- cima.segments.segment_features module
- cima.segments.segment_gaussian module
- cima.segments.segment_info_h5 module
- cima.segments.segment_info_xyz module
SegmentXYZSegmentXYZ.Getcoord()SegmentXYZ.TimesIDs()SegmentXYZ.calculate_centre_of_mass()SegmentXYZ.calculate_centroid()SegmentXYZ.copy()SegmentXYZ.copyWithNewContent()SegmentXYZ.getClusters()SegmentXYZ.getInRange()SegmentXYZ.getPortion()SegmentXYZ.get_Cluster_segment()SegmentXYZ.get_Time_segment()SegmentXYZ.get_extreme_values()SegmentXYZ.get_multiple_Time_segment()SegmentXYZ.get_vector_list()SegmentXYZ.no_of_Cluster()SegmentXYZ.no_of_Times()SegmentXYZ.removeNoise()SegmentXYZ.renumberTimeFromInt()SegmentXYZ.renumber_Time()SegmentXYZ.representSingleLocalization()SegmentXYZ.set_cluster_ids()SegmentXYZ.splitByValue()SegmentXYZ.split_into_Clusters()SegmentXYZ.split_into_time()
- cima.segments.segment_info module
SegmentSegment.ChromosomesIDs()Segment.GetMaxAccuracy()Segment.GetMaxPrecision()Segment.GetMeanAccuracy()Segment.GetMeanPrecision()Segment.GetMinAccuracy()Segment.GetMinPrecision()Segment.OrderbyExperimenttime()Segment.PSFz_shiftFilter()Segment.PhotonCount_Filter()Segment.PrecisionFilter()Segment.copy()Segment.copyWithNewContent()Segment.getFrames()Segment.get_Chromosomes_segment()Segment.no_of_Chromosomes()Segment.representSingleLocalization()Segment.set_chromosomes()Segment.split_into_Chromosomes()Segment.split_into_cycle()Segment.split_into_frames_chunk()
- cima.segments.segment_spatial_features module
- cima.utils package
- Submodules
- cima.utils.matrices_comparison module
- cima.utils.misc module
- cima.utils.stats_function module
Create_Random_Hom_Ratio()Create_Random_Hom_Ratio_Paternal_Origin()Create_Random_Hom_Ratio_largeroversmaller()Create_Random_Hom_Ratio_smalloverlarger()func()func2()func_inverse1()func_powerlaw()func_sqrt()getLogLinearRegression()makeAxesLabelsLog()plotLine()plotLogWithKdeColors()power_law()statConvert()welch_ttest()
- cima.utils.vector module
- cima.utils.visualization module
- cima.utils.walk_features module
MeanMatrix()convertToFreq()convertToMatrix()convertToMatrix2()getEigenvecsFromContactMat()getMergedMorphologicalAndSpatialSegmentsFeatures()getSegmentFeatures()getSegmentMetadata()getSegmentsFeatures()getSegmentsMetadata()getSegmentsPairFeatures()getSpatialFeaturesInterWalk()getSpatialFeaturesIntraWalk()
- cima.utils.write_pdb module