Index

A

ablation_distance_between_shots_x (AcquisitionDict attribute) ablation_distance_between_shots_y (AcquisitionDict attribute) ablation_frequency (AcquisitionDict attribute) ablation_power (AcquisitionDict attribute) AblationImageType (class in imctools.data.acquisition) Acquisition (class in imctools.data.acquisition) acquisition() (AcquisitionData property)

acquisition_id (ChannelDict attribute) acquisition_ids() (Session property) AcquisitionData (class in imctools.data.acquisitiondata) AcquisitionDict (class in imctools.data.acquisition) acquisitions (SessionDict attribute) AFTER (AblationImageType attribute) analysis_stacks (imctools.converters.omefolder_to_analysisfolder parameter)

B

base_folder (imctools.cli.omefile_to_histocatfolder parameter) (imctools.converters.omefile_to_histocatfolder parameter) basename (imctools.cli.omefile_2_analysisfolder parameter) (imctools.cli.omefile_to_tifffolder parameter) (imctools.converters.omefile_2_analysisfolder parameter) (imctools.converters.omefile_to_tifffolder parameter) (imctools.data.acquisitiondata.AcquisitionData.save_tiffs parameter)

BEFORE (AblationImageType attribute) bigtiff (imctools.cli.omefile_2_analysisfolder parameter) (imctools.converters.omefile_2_analysisfolder parameter) (imctools.data.acquisitiondata.AcquisitionData.save_tiffs parameter)

C

Channel (class in imctools.data.channel) channel_indices (imctools.io.utils.reshape_long_2_cyx parameter) channel_labels() (Acquisition property) (AcquisitionData property) channel_masses() (Acquisition property) (AcquisitionData property) channel_names() (Acquisition property) (AcquisitionData property)

ChannelDict (class in imctools.data.channel) channels (SessionDict attribute) close() (McdParser method) compression (imctools.data.acquisitiondata.AcquisitionData.save_tiffs parameter) create_zip (imctools.cli.mcdfolder_to_imcfolder parameter) (imctools.converters.mcdfolder_to_imcfolder parameter) created (SessionDict attribute)

D

data (imctools.io.utils.reshape_long_2_cyx parameter) description (AcquisitionDict attribute) (PanoramaDict attribute) (SlideDict attribute) dtype (imctools.cli.omefile_2_analysisfolder parameter) (imctools.cli.omefile_to_histocatfolder parameter) (imctools.cli.omefile_to_tifffolder parameter) (imctools.cli.omefolder_to_histocatfolder parameter) (imctools.converters.omefile_2_analysisfolder parameter) (imctools.converters.omefile_to_histocatfolder parameter) (imctools.converters.omefile_to_tifffolder parameter) (imctools.converters.omefolder_to_analysisfolder parameter) (imctools.converters.omefolder_to_histocatfolder parameter) (imctools.data.acquisitiondata.AcquisitionData.save_ome_tiff parameter) (imctools.data.acquisitiondata.AcquisitionData.save_tiffs parameter)

E

end_timestamp (AcquisitionDict attribute) export_acquisition_csv() (in module imctools.cli) (in module imctools.converters)

extract_acquisition_id() (OmeTiffParser static method) (TxtParser static method)

F

filename (imctools.cli.omefile_2_analysisfolder parameter) (imctools.converters.omefile_2_analysisfolder parameter) (imctools.data.acquisitiondata.AcquisitionData.save_ome_tiff parameter) filename() (Slide property) filepath (imctools.cli.omefile_to_histocatfolder parameter) (imctools.cli.omefile_to_tifffolder parameter) (imctools.converters.omefile_to_histocatfolder parameter) (imctools.converters.omefile_to_tifffolder parameter) (imctools.data.session.Session.load parameter) (imctools.data.session.Session.save parameter) (imctools.io.ometiff.ometiffparser.OmeTiffParser.extract_acquisition_id parameter) (imctools.io.txt.txtparser.TxtParser.extract_acquisition_id parameter)

filepath() (OmeTiffParser property) (TxtParser property) folder_name() (ImcWriter property) from_dict() (Acquisition static method) (Channel static method) (Panorama static method) (Session static method) (Slide static method)

G

get_acquisition_data() (ImcParser method) (McdParser method) (OmeTiffParser method) (TxtParser method) get_after_ablation_image() (McdParser method) get_before_ablation_image() (McdParser method) get_csv_dict() (Acquisition method) (Channel method) (Panorama method) (Session method) (Slide method) get_image_by_index() (AcquisitionData method) get_image_by_label() (AcquisitionData method)

get_image_by_name() (AcquisitionData method) get_image_stack_by_indices() (AcquisitionData method) get_image_stack_by_labels() (AcquisitionData method) get_image_stack_by_names() (AcquisitionData method) get_mass_indices() (Acquisition method) get_mcd_xml() (ImcParser method) (McdParser method) (McdXmlParser method) (OmeTiffParser method) get_name_indices() (Acquisition method) get_ome_xml() (in module imctools.io.utils) get_panorama_image() (McdParser method) get_slide_image() (McdParser method)

H

has_after_ablation_image (AcquisitionDict attribute) has_before_ablation_image (AcquisitionDict attribute)

has_slide_image (SlideDict attribute) height_um (SlideDict attribute)

I

id (AcquisitionDict attribute) (ChannelDict attribute) (PanoramaDict attribute) (SessionDict attribute) (SlideDict attribute) image_data() (AcquisitionData property) image_type (PanoramaDict attribute) imagej (imctools.data.acquisitiondata.AcquisitionData.save_tiffs parameter) ImcParser (class in imctools.io.imc.imcparser) imctools.cli module imctools.converters module imctools.data.acquisition module imctools.data.acquisitiondata module imctools.data.channel module imctools.data.panorama module imctools.data.session module imctools.data.slide module imctools.io.imc.imcparser module

imctools.io.imc.imcwriter module imctools.io.mcd.constants module imctools.io.mcd.mcdparser module imctools.io.mcd.mcdxmlparser module imctools.io.ometiff.ometiffparser module imctools.io.txt.txtparser module imctools.io.utils module imctools_version (SessionDict attribute) ImcWriter (class in imctools.io.imc.imcwriter) input (imctools.cli.mcdfolder_to_imcfolder parameter) (imctools.converters.mcdfolder_to_imcfolder parameter) input_folder (imctools.cli.omefolder_to_histocatfolder parameter) (imctools.cli.v1_to_v2 parameter) (imctools.converters.omefolder_to_analysisfolder parameter) (imctools.converters.omefolder_to_histocatfolder parameter) (imctools.converters.v1_to_v2 parameter) is_sorted (imctools.io.utils.reshape_long_2_cyx parameter) is_valid (AcquisitionDict attribute) is_valid() (AcquisitionData property)

L

label (ChannelDict attribute)

load() (Session static method)

M

main() (in module imctools.cli) mask_file (imctools.cli.omefile_to_histocatfolder parameter) (imctools.converters.omefile_to_histocatfolder parameter) mask_folder (imctools.cli.omefolder_to_histocatfolder parameter) (imctools.converters.omefolder_to_histocatfolder parameter) mask_suffix (imctools.cli.omefolder_to_histocatfolder parameter) (imctools.converters.omefolder_to_histocatfolder parameter) mass (ChannelDict attribute) masses (imctools.data.acquisitiondata.AcquisitionData.save_ome_tiff parameter) (imctools.data.acquisitiondata.AcquisitionData.save_tiffs parameter) max_intensity (ChannelDict attribute) max_x (AcquisitionDict attribute) max_y (AcquisitionDict attribute) mcd_filename() (McdParser property) mcdfolder_to_imcfolder() (in module imctools.cli) (in module imctools.converters) McdParser (class in imctools.io.mcd.mcdparser) McdXmlParser (class in imctools.io.mcd.mcdxmlparser) metadata (AcquisitionDict attribute) (ChannelDict attribute) (PanoramaDict attribute) (SessionDict attribute) (SlideDict attribute) metalcolumn (imctools.cli.omefile_2_analysisfolder parameter) (imctools.converters.omefile_2_analysisfolder parameter) (imctools.converters.omefolder_to_analysisfolder parameter)

metaname() (Acquisition property) (Channel property) (Panorama property) (Session property) (Slide property) min_intensity (ChannelDict attribute) module imctools.cli imctools.converters imctools.data.acquisition imctools.data.acquisitiondata imctools.data.channel imctools.data.panorama imctools.data.session imctools.data.slide imctools.io.imc.imcparser imctools.io.imc.imcwriter imctools.io.mcd.constants imctools.io.mcd.mcdparser imctools.io.mcd.mcdxmlparser imctools.io.ometiff.ometiffparser imctools.io.txt.txtparser imctools.io.utils movement_type (AcquisitionDict attribute)

N

n_channels() (Acquisition property) (AcquisitionData property) name (ChannelDict attribute) (SessionDict attribute)

name() (Slide property) names (imctools.data.acquisitiondata.AcquisitionData.save_ome_tiff parameter) (imctools.data.acquisitiondata.AcquisitionData.save_tiffs parameter)

O

omefile_2_analysisfolder() (in module imctools.cli) (in module imctools.converters) omefile_to_histocatfolder() (in module imctools.cli) (in module imctools.converters) omefile_to_tifffolder() (in module imctools.cli) (in module imctools.converters) omefolder_to_analysisfolder() (in module imctools.converters) omefolder_to_histocatfolder() (in module imctools.cli) (in module imctools.converters) OmeTiffParser (class in imctools.io.ometiff.ometiffparser) order_number (ChannelDict attribute) origin (AcquisitionDict attribute) origin() (ImcParser property) (McdParser property) (McdXmlParser property) (OmeTiffParser property) (TxtParser property)

output_folder (imctools.cli.export_acquisition_csv parameter) (imctools.cli.mcdfolder_to_imcfolder parameter) (imctools.cli.omefile_2_analysisfolder parameter) (imctools.cli.omefile_to_tifffolder parameter) (imctools.cli.omefolder_to_histocatfolder parameter) (imctools.cli.v1_to_v2 parameter) (imctools.converters.export_acquisition_csv parameter) (imctools.converters.mcdfolder_to_imcfolder parameter) (imctools.converters.omefile_2_analysisfolder parameter) (imctools.converters.omefile_to_tifffolder parameter) (imctools.converters.omefolder_to_analysisfolder parameter) (imctools.converters.omefolder_to_histocatfolder parameter) (imctools.converters.v1_to_v2 parameter) (imctools.data.acquisitiondata.AcquisitionData.save_tiffs parameter) output_name (imctools.cli.export_acquisition_csv parameter) (imctools.converters.export_acquisition_csv parameter)

P

panel_csv_file (imctools.cli.omefile_2_analysisfolder parameter) (imctools.converters.omefile_2_analysisfolder parameter) (imctools.converters.omefolder_to_analysisfolder parameter) Panorama (class in imctools.data.panorama)

PanoramaDict (class in imctools.data.panorama) panoramas (SessionDict attribute) parse_txt (imctools.cli.mcdfolder_to_imcfolder parameter) (imctools.converters.mcdfolder_to_imcfolder parameter)

R

reshape_long_2_cyx() (in module imctools.io.utils) roi_end_x_pos_um (AcquisitionDict attribute) roi_end_y_pos_um (AcquisitionDict attribute) roi_start_x_pos_um (AcquisitionDict attribute)

roi_start_y_pos_um (AcquisitionDict attribute) root_folder (imctools.cli.export_acquisition_csv parameter) (imctools.converters.export_acquisition_csv parameter) rotation_angle (PanoramaDict attribute)

S

save() (Session method) save_after_ablation_image() (McdParser method) save_before_ablation_image() (McdParser method) save_meta_csv() (Session method) save_ome_tiff() (AcquisitionData method) save_panorama_image() (McdParser method) save_slide_image() (McdParser method) save_tiff() (AcquisitionData method) save_tiffs() (AcquisitionData method) segment_data_format (AcquisitionDict attribute) Session (class in imctools.data.session) session() (ImcParser property) (McdParser property) (McdXmlParser property) session_id (SlideDict attribute) SessionDict (class in imctools.data.session)

shape (imctools.io.utils.reshape_long_2_cyx parameter) signal_type (AcquisitionDict attribute) Slide (class in imctools.data.slide) slide_id (AcquisitionDict attribute) (PanoramaDict attribute) SlideDict (class in imctools.data.slide) slides (SessionDict attribute) sort_acquisition_channels() (in module imctools.io.utils) sort_channels (imctools.cli.omefile_2_analysisfolder parameter) (imctools.converters.omefile_2_analysisfolder parameter) source_path (AcquisitionDict attribute) start_timestamp (AcquisitionDict attribute) sw_version() (Slide property) symbol (Acquisition attribute) (Channel attribute) (Panorama attribute) (Slide attribute)

T

template (AcquisitionDict attribute)

to_xarray() (AcquisitionData method) TxtParser (class in imctools.io.txt.txtparser)

U

uid() (Slide property)

usedcolumn (imctools.cli.omefile_2_analysisfolder parameter) (imctools.converters.omefile_2_analysisfolder parameter)

V

v1_to_v2() (in module imctools.cli) (in module imctools.converters)

W

width_um (SlideDict attribute)

write_imc_folder() (ImcWriter method)

X

x1 (PanoramaDict attribute) x2 (PanoramaDict attribute)

x3 (PanoramaDict attribute) x4 (PanoramaDict attribute) xml_metadata (imctools.data.acquisitiondata.AcquisitionData.save_ome_tiff parameter)

Y

y1 (PanoramaDict attribute) y2 (PanoramaDict attribute)

y3 (PanoramaDict attribute) y4 (PanoramaDict attribute)