pycytominer

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Gaussianize feature values with inverse normalize transform (INT)

2

We used this transformation in a paper in preparation, it would be great to add this functionality to pycytominer to enable all future users access! cc @jatinarora-upmc @shntnu

gwaybio

Modular single cell ingest

1

As currently defined in [aggregate.py](https://github.com/cytomining/pycytominer/blob/ac3ef680c1f4625aa1e8452b431afb5af8bcdd41/pycytominer/aggregate.py), the class `AggregateProfiles()` works using SQLite files only. We have added [`parquet`](https://parquet.apache.org/) functionality in cytomining/cytominer-database#122 and are finalizing the addition in cytomining/cytominer-database#130. The task in...

gwaybio

Refactor out data reading functionality

1

In #202 we discussed refactoring the [`SingleCells`](https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/cells.py#L25) data reading functionality into a new, separate utility. This refactoring is likely to farther unscramble SQLite from this repo enabling a smoother sunset....

gwaybio

Should pycytominer generate additional metadata columns by default?

3

In #129, @niranjchandrasekaran proposed that pycytominer create a metadata column, called `Metadata_fields_count`, that will be added to all future pycytominer-derived aggregate profiles. This represents the first time (IIRC) that pycytominer...

gwaybio

`count_cells` function unable to work with SQLite file without TableNumber

1

When trying to use the `count_cells` function within the [cells.py](https://github.com/cytomining/pycytominer/blob/b2c6cc4580cf9e1c040a7370b99976916a22e756/pycytominer/cyto_utils/cells.py#L305) file, I am coming across this error: ``` OperationalError: (sqlite3.OperationalError) no such table: cells [SQL: select TableNumber, ImageNumber, ObjectNumber from...

jenna-tomkinson

Bug: `SingleCells` class will not extract image features

1

I have been using the SingleCells class from pycytominer cells.py file to extract image and object features measured with CellProfiler. I noticed that the image features were not being extracted...

jenna-tomkinson

[Enhancement] Expose primary functions (annotate, feature_select, etc.) as CLI commands

2

For the purposes of integrating pycytominer into data pipelines like Nextflow it would be great if core functionality could be exposed via a CLI. The quickest way to implement this...

kenibrewer

`annotate` function kills kernel when trying to process a 13.1GB file

2

This issue is related to issue #233. I created a group of Python files to: 1. Convert the two CellProfiler SQLite outputs into parquet and merge single cells using [CytoTable...

jenna-tomkinson

Increase test coverage of cell_locations by figuring out how to use `moto`

1

The test coverage of `cyto_utils.cell_locations` can be increased to 100% if we figure out how to use `moto`. More here: https://github.com/cytomining/pycytominer/pull/257#issuecomment-1446184844

shntnu

Context: https://github.com/cytomining/pycytominer/pull/257#issuecomment-1493329598 Refactoring `SingleCells` would expose more reusable functionality that `CellLocations` (and other future classes) could benefit from. For example, some of these `CellLocations` methods could be moved into `SingleCells`...

shntnu