Data · dataset · 2024
cryo-ET tutorial dataset for template matching
Listed in IISH Dataverse
The dataset is intended for the pytom-gpu-template-matching module for running GPU-accelerated template matching.
Description
Details of the method can be found in Chaillet et al., 2023. The dataset contains 10 tomographic reconstruction from cryo-electron microscopy tilt-series.
The reconstruction were generated as follows: (1) MotionCor2 was used to correct the motion in raw movie frames, (2) ctfplotter from IMOD was used to estimate defocus values, (3) ctfphaseflip from IMOD was used for strip-based phaseflipping, and (4) AreTomo was used to align and reconstruct tomograms (weighted back-projection) with 5x5 local patches. Files are saved in the MRC format and the name has the structure tomo[DATE]_[ID].mrc, where DATE refers to collection date and ID refers to the tilt-series index.
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Each tomogram additionally contains three files using the same name format, but ending in .rawtlt, .defocus, and _dose.txt. These files contain tilt-angles used for collecting the tilt-series (in degrees), accumulated dose per tilt (in e-/A2), and an IMOD-style defocus files with estimated defocus per tilt, respectively. Each tomogram also contains a STAR file with manually inspected and corrected annotations, resembling some sort of a 'ground truth' annotation.
The files end with *_bin_manual.star and are in the Relion4 STAR format. The tutorial and software can be found on Github: tutorial instructions download software The raw tilt-series can be found in this DataverseNL repository doi:10.34894/OLYEFI, they were collected as described in Gemmer et al., 2023 for which there is an EMPIAR dataset available EMPIAR-11751.
Links
Where it is published
- Dataverse dataset page dataverse.nl/dataset.xhtml?persistentId=doi%3A10.34894%2FTLGJCM ↗
landing page · from datasets iisg amsterdam
- DOI doi.org/10.34894/tlgjcm ↗
DOI / persistent id · from datasets iisg amsterdam
Catalogue records · 1
- Dataverse API dataverse.nl/api/datasets/:persistentId/?persistentId=doi%3A10.34894%2FTLGJ… ↗
metadata API · from datasets iisg amsterdam
Topics
- Stated by source
- Computer and Information Science · Medicine, Health and Life Sciences
- From keywords
- Life Sciences · Medicine & Health
- Inferred from text
- Microscopy 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| IISH Dataverse | doi:10.34894/TLGJCM | 8 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].dataverse_subject:computer-and-information-science | source · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | /subjects |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | /subjects |
| concepts[modality].local:modality:microscopy | enrichment · datasets iisg amsterdam | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | |
| description | source · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | /description |
| publication_date | source · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | |
| title | source · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | /name |
| updated_date | source · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 | |
| version_label | source · datasets iisg amsterdam | connector:datasets_iisg_amsterdam@1.0.0 |