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Add Annotation Importer for Instance segmentations. #31
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A config file to test with current ingestion tools: dataset:
dataset_identifier: 10002
dataset_description: "Cryo-electron tomograms of RPE1 cells. Comprehensive annotation of actin filaments and microtubules"
dataset_title: RPE1 cytosol with actin stress fiber
authors: &dataset_authors
- name: Irene de Teresa Trueba
ORCID: 0000-0002-4691-9501
primary_author_status: true
- name: Sara Goetz
ORCID: 0000-0002-9903-3667
- name: Alexander Mattausch
ORCID: 0000-0003-0901-8701
- name: Frosina Stojanovska
ORCID: 0000-0002-4327-1068
- name: Christian Eugen Zimmerli
ORCID: 0000-0003-4388-1349
- name: Mauricio Toro-Nahuelpan
ORCID: 0000-0001-5333-3640
- name: Dorothy W. C. Cheng
- name: Fergus Tollervey
- name: Constantin Pape
ORCID: 0000-0001-6562-7187
- name: Martin Beck
ORCID: 0000-0002-7397-1321
- name: Alba Diz-Munoz
ORCID: 0000-0001-6864-8901
- name: Anna Kreshuk
ORCID: 0000-0003-1334-6388
- name: Julia Mahamid
ORCID: 0000-0001-6968-041X
corresponding_author_status: true
- name: Judith B. Zaugg
ORCID: 0000-0001-8324-4040
corresponding_author_status: true
cross_references:
dataset_publications: &publications doi:10.1101/2022.04.12.488077, doi:10.1038/s41592-022-01746-2
related_database_entries: EMPIAR-10989
cell_component:
name: ~
id: ~
cell_type:
id: CL:0002586
name: Retinal pigment epithelial-1
dates: &repo-dates
deposition_date: 2023-05-01
last_modified_date: 2023-11-08
release_date: 2023-11-30
funding:
- funding_agency_name: European Research Council (ERC)
grant_id: '760067'
grid_preparation: 'model: Quantifoil, material: GOLD, support_film_film_type_id: 1, support_film_film_topology: HOLEY, support_film_instance_type: support_film, pretreatment_type_: PLASMA CLEANING'
key_photos:
snapshot: https://www.ebi.ac.uk/pdbe/emdb-empiar/entryIcons/10989-l.gif
thumbnail: https://www.ebi.ac.uk/pdbe/emdb-empiar/entryIcons/10989.gif
organism:
name: Homo sapiens
taxonomy_id: 9606
sample_preparation: 'buffer_ph: 7.4, vitrification_cryogen_name: ETHANE, cryo_protectant: None, instance_type: tomography_preparation'
sample_type: cell
tissue:
id: BTO:0001175
name: retina
runs: {}
tiltseries:
acceleration_voltage: 300000
binning_from_frames: 1
camera:
manufacturer: Gatan
model: K2 SUMMIT
data_acquisition_software: SerialEM
microscope:
manufacturer: TFS
model: KRIOS
microscope_optical_setup:
energy_filter: GIF Quantum LS
phase_plate: VOLTA PHASE PLATE
image_corrector: null
pixel_spacing: '{run_pixel_spacing}'
related_empiar_entry: ~
scales: []
spherical_aberration_constant: 2.7
tilting_scheme: Dose symmetric from 0.0 degrees
tilt_axis: 79
tilt_range:
min: -60
max: 60
tilt_step: 3
tilt_series_quality: 5
total_flux: 125
is_aligned: false
alignment_binning_factor: ~ # We may need to calculate this for each tilt if we can identify aligned & unaligned files in the bucket.
tomograms:
ctf_corrected: false
fiducial_alignment_status: NON_FIDUCIAL
offset:
x: 0
y: 0
z: 0
affine_transformation_matrix: [[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, -1, 0], [0, 0, 625, 1]] # TODO - this is different per tomo
processing: raw
reconstruction_method: Weighted back projection
reconstruction_software: IMOD
tomogram_version: 1
authors: *dataset_authors
voxel_spacing: '{run_voxel_spacing}'
annotations:
- metadata:
annotation_object:
id: GO:0016020
name: membrane
description: ~
state: ~
dates: *repo-dates
annotation_method: TARDIS
method_type: automated
annotation_publications: ~
ground_truth_status: False
authors: &annotation_authors
- name: Robert Kiewisz
primary_annotator_status: true
- name: Tristan Bepler
corresponding_author_status: true
annotation_software: TARDIS
version: '1.0'
confidence:
precision: ~
recall: ~
is_curator_recommended: False
sources:
- file_format: tardis
binning: 1
order: xyz
shape: InstanceSegmentation
glob_string: 10002/{run_name}/{run_name}_instance.csv
is_visualization_default: false
- metadata:
dates: *repo-dates
annotation_method: TARDIS
method_type: automated
annotation_publications: *publications
ground_truth_status: False
authors: *annotation_authors
annotation_software: TARDIS
version: '1.0'
confidence:
precision: ~
recall: ~
ground_truth_used: ~
annotation_object:
id: GO:0016020
name: membrane
description: ~
state: ~
is_curator_recommended: false
sources:
- file_format: mrc
shape: SemanticSegmentationMask
glob_string: 10002/{run_name}/{run_name}_semantic.mrc
is_visualization_default: false
overrides_by_run:
- run_regex: "^00011$"
tiltseries:
pixel_spacing: 3.45
tomograms:
voxel_spacing: 13.8
- run_regex: "^00012$"
tiltseries:
pixel_spacing: 3.45
tomograms:
voxel_spacing: 13.8
standardization_config:
destination_prefix: '10002_robert'
source_prefix: julia_test/RPE1/RPE1
run_to_frame_map_csv: run_to_frame_name_map.csv
gain_glob: CountRef_{mapped_frame_name}-range.dm4
frames_glob: frames/{mapped_frame_name}_*.tif
rawtlt_files:
- metadata/{run_name}_sq_df_sorted_fid.xf
- metadata/{run_name}.mdoc
tiltseries_glob: stack/{run_name}_sq_df_sorted_orig.st
tomo_format: mrc
tomo_glob: tomograms/{run_name}_*.rec
tomo_voxel_size: ''
run_glob: tomograms/*.rec
run_regex: .*
run_name_regex: (.*)_sq_df_sorted.rec
run_data_map_file: run_data_map.csv |
In creating this for the short term I have some thoughts on how we import point annotations:
|
manasaV3
approved these changes
Mar 22, 2024
jgadling
approved these changes
Mar 22, 2024
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Imports TARDIS instance points, new point formate with the additional label "instance_id".