jump-portrait 0.0.16

Tools to fetch and visualize JUMP images

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

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