| Name | jump-portrait JSON |
| Version |
0.0.16
JSON |
| download |
| home_page | None |
| Summary | Tools to fetch and visualize JUMP images |
| upload_time | 2024-05-02 19:39:11 |
| maintainer | None |
| docs_url | None |
| author | Alan Munoz |
| requires_python | <4.0,>=3.9 |
| license | None |
| keywords |
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Table of Contents
Tools to fetch and visualize images from the JUMP dataset.
## Workflow
### User
### Developer
Locate the images that correspond to a given gene
```python
from jump_portrait.fetch import get_item_location_info
gene = "MYT1"
location_df = get_item_location_info(gene)
Returns a polars dataframe whose columns contain the metadata
alongside path and file locations
#┌───────────┬───────────┬───────────┬───────────┬───┬───────────┬───────────┬───────────┬──────────┐
#│ Metadata_ ┆ Metadata_ ┆ Metadata_ ┆ Metadata_ ┆ … ┆ PathName_ ┆ Metadata_ ┆ Metadata_ ┆ standard │
#│ Source ┆ Batch ┆ Plate ┆ Well ┆ ┆ OrigRNA ┆ PlateType ┆ JCP2022 ┆ _key │
#│ --- ┆ --- ┆ --- ┆ --- ┆ ┆ --- ┆ --- ┆ --- ┆ --- │
#│ str ┆ str ┆ str ┆ str ┆ ┆ str ┆ str ┆ str ┆ str │
#╞═══════════╪═══════════╪═══════════╪═══════════╪═══╪═══════════╪═══════════╪═══════════╪══════════╡
#│ source_13 ┆ 20220914_ ┆ CP-CC9-R1 ┆ B05 ┆ … ┆ s3://cell ┆ CRISPR ┆ JCP2022_8 ┆ MYT1 │
#│ ┆ Run1 ┆ -20 ┆ ┆ ┆ painting- ┆ ┆ 04400 ┆ │
#│ ┆ ┆ ┆ ┆ ┆ gallery/c ┆ ┆ ┆ │
#│ ┆ ┆ ┆ ┆ ┆ pg001… ┆ ┆ ┆ │
#│ source_13 ┆ 20220914_ ┆ CP-CC9-R1 ┆ B05 ┆ … ┆ s3://cell ┆ CRISPR ┆ JCP2022_8 ┆ MYT1 │
#│ ┆ Run1 ┆ -20 ┆ ┆ ┆ painting- ┆ ┆ 04400 ┆ │
#│ ┆ ┆ ┆ ┆ ┆ gallery/c ┆ ┆ ┆ │
#│ ┆ ┆ ┆ ┆ ┆ pg001… ┆ ┆ ┆ │
#│ source_13 ┆ 20220914_ ┆ CP-CC9-R1 ┆ B05 ┆ … ┆ s3://cell ┆ CRISPR ┆ JCP2022_8 ┆ MYT1 │
#│ ┆ Run1 ┆ -20 ┆ ┆ ┆ painting- ┆ ┆ 04400 ┆ │
#│ ┆ ┆ ┆ ┆ ┆ gallery/c ┆ ┆ ┆ │
#│ ┆ ┆ ┆ ┆ ┆ pg001… ┆ ┆ ┆ │
#│ source_13 ┆ 20220914_ ┆ CP-CC9-R1 ┆ B05 ┆ … ┆ s3://cell ┆ CRISPR ┆ JCP2022_8 ┆ MYT1 │
#│ ┆ Run1 ┆ -20 ┆ ┆ ┆ painting- ┆ ┆ 04400 ┆ │
#│ ┆ ┆ ┆ ┆ ┆ gallery/c ┆ ┆ ┆ │
#│ ┆ ┆ ┆ ┆ ┆ pg001… ┆ ┆ ┆ │
#│ source_13 ┆ 20220914_ ┆ CP-CC9-R1 ┆ B05 ┆ … ┆ s3://cell ┆ CRISPR ┆ JCP2022_8 ┆ MYT1 │
#│ ┆ Run1 ┆ -20 ┆ ┆ ┆ painting- ┆ ┆ 04400 ┆ │
#│ ┆ ┆ ┆ ┆ ┆ gallery/c ┆ ┆ ┆ │
#│ ┆ ┆ ┆ ┆ ┆ pg001… ┆ ┆ ┆ │
#└───────────┴───────────┴───────────┴───────────┴───┴───────────┴───────────┴───────────┴──────────┘
```
The columns of these dataframes are:
```
Metadata_[Source/Batch/Plate/Well/Site]:
- Source: Source in the range 0-14.
- Plate:
- Batch:
- Well:
- Site: Foci or frame taken in a the well, generally these are 0-9.
[File/Path]name_[Illum/Orig][Channel]
- Illum: Illumination correction
- Orif: Original File
Also, markers can be:
- DNA: Dna channel, generally Hoecsht.
- ER: Endoplasmatic Reticulum channel.
- Mito: Mitochondrial channel.
- RNA: RNA channel.
standard_key: Gene or compound queried
```
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