Jenna Tomkinson
Jenna Tomkinson
As I was working with the RunCellpose plugin in CellProfiler, I noticed that there was a function missing that is normally available in the `IdentifyPrimaryObjects` and `IdentifySecondaryObjects` modules, which is...
I have added the `remove_edge_masks` function as described in #168. This will allow the user the same functionality that is provided in the `IdentifyPrimaryObjects` and `IdentifySecondaryObjects` modules (e.g. remove objects/cells/nuclei...
## Installation and Functionality Problems with Cellpose Plugin: My goal is to compare Cellpose stand-alone to the Cellpose plugin inside CellProfiler But, I have run into many issues, ranging from...
**Describe the bug** I am noticing that the MeasureColocalization module in my pipelines has significantly increased (by about 720%) in run time both `CPU_time` and `wall_time`, compared to just a...
**Is your feature request related to a problem? Please describe.** This feature request isn't one that solves a problem, it is adding to the functionality of CellProfiler as a whole....
### Feature type - [X] Add new functionality - [ ] Change existing functionality ### General description of the proposed functionality @axiomcura first discovered this issue. Currently, when using the...
### Example code with output ```python # normalize annotated data normalized_df = normalize( # df with annotated raw merged single cell features profiles=annotated_df, # normalization method used method="standardize" ) ```...
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...
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...
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...