kfm 1.0.2

A better way to manage Keyence-generated microscopy data

keyence_file_management

kfm is a helper package that helps reorganize Keyence files and folders to make labeling and finding images taken by the Keyence easier.

Here's an example of what an example Keyence folder looks like before and after using kfm.

.
├── A01.lnk
├── B01.lnk
├── C01.lnk
├── D01.lnk
├── E01.lnk
├── F01.lnk
├── G01.lnk
├── XY01
│   ├── 2021.07.29_293T_4X_XY01_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_XY01_00001_CH4.tif
│   ├── 2021.07.29_293T_4X_XY01_00001_Overlay.tif
│   └── _A01
├── XY02
│   ├── 2021.07.29_293T_4X_XY02_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_XY02_00001_CH4.tif
│   ├── 2021.07.29_293T_4X_XY02_00001_Overlay.tif
│   └── _B01
├── XY03
│   ├── 2021.07.29_293T_4X_XY03_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_XY03_00001_CH4.tif
│   ├── 2021.07.29_293T_4X_XY03_00001_Overlay.tif
│   └── _C01
├── XY04
│   ├── 2021.07.29_293T_4X_XY04_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_XY04_00001_CH4.tif
│   ├── 2021.07.29_293T_4X_XY04_00001_Overlay.tif
│   └── _D01
├── XY05
│   ├── 2021.07.29_293T_4X_XY05_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_XY05_00001_CH4.tif
│   ├── 2021.07.29_293T_4X_XY05_00001_Overlay.tif
│   └── _E01
├── XY06
│   ├── 2021.07.29_293T_4X_XY06_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_XY06_00001_CH4.tif
│   ├── 2021.07.29_293T_4X_XY06_00001_Overlay.tif
│   └── _F01
├── XY07
│   ├── 2021.07.29_293T_4X_XY07_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_XY07_00001_CH4.tif
│   ├── 2021.07.29_293T_4X_XY07_00001_Overlay.tif
│   └── _G01
└── key.yaml

.
├── pMXs-eGFP-MODC
│   ├── 2021.07.29_293T_4X_G01_pMXs-eGFP-MODC_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_G01_pMXs-eGFP-MODC_00001_CH4.tif
│   └── 2021.07.29_293T_4X_G01_pMXs-eGFP-MODC_00001_Overlay.tif
├── pMXs-eGFP-WPRE
│   ├── 2021.07.29_293T_4X_F01_pMXs-eGFP-WPRE_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_F01_pMXs-eGFP-WPRE_00001_CH4.tif
│   └── 2021.07.29_293T_4X_F01_pMXs-eGFP-WPRE_00001_Overlay.tif
├── pMXs-mGL
│   ├── 2021.07.29_293T_4X_A01_pMXs-mGL_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_A01_pMXs-mGL_00001_CH4.tif
│   └── 2021.07.29_293T_4X_A01_pMXs-mGL_00001_Overlay.tif
├── pMXs-mGL-MODC
│   ├── 2021.07.29_293T_4X_B01_pMXs-mGL-MODC_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_B01_pMXs-mGL-MODC_00001_CH4.tif
│   └── 2021.07.29_293T_4X_B01_pMXs-mGL-MODC_00001_Overlay.tif
├── pMXs-mGL-MODC_mut
│   ├── 2021.07.29_293T_4X_C01_pMXs-mGL-MODC_mut_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_C01_pMXs-mGL-MODC_mut_00001_CH4.tif
│   └── 2021.07.29_293T_4X_C01_pMXs-mGL-MODC_mut_00001_Overlay.tif
├── pMXs-mGL-UbR
│   ├── 2021.07.29_293T_4X_E01_pMXs-mGL-UbR_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_E01_pMXs-mGL-UbR_00001_CH4.tif
│   └── 2021.07.29_293T_4X_E01_pMXs-mGL-UbR_00001_Overlay.tif
├── pMXs-mGL-Ubi-Y-dK
│   ├── 2021.07.29_293T_4X_D01_pMXs-mGL-Ubi-Y-dK_00001_CH2.tif
│   ├── 2021.07.29_293T_4X_D01_pMXs-mGL-Ubi-Y-dK_00001_CH4.tif
│   └── 2021.07.29_293T_4X_D01_pMXs-mGL-Ubi-Y-dK_00001_Overlay.tif
├── record.json
└── unmoved

Install

This package is on PyPI, so just:

pip install kfm

Usage

kfm has a command-line interface:

usage: kfm [-h] [-rev | --opt group_by_options] [--ypath yaml_path] group_folder_path

Required Arguments

group_folder_path: The path to where the group folder is. Group folders are one level above the XY folders, e.g. group_folder_path / XY01 / *.tif

Optional Arguments

--rev: Include this argument to reverse a move. The record.json file generated during the move must be in the specified group_folder_path.

--opt [group_by_opts]: Include this argument to specify how folders are nested. This can be provided as a single option (e.g. 'cond') or as a list where the order of the list specifies the order of the folder nessting. For exampple, --opt ['cond', 'T'] nests folders by conditions / time point whereas --opt ['T', 'cond'] nests folders by time point / condition. The record.json file generated during the move must be in the specified group_folder_path. Posssible options are: ['none', 'XY', 'cond', 'T', 'stitch', 'Z', 'CH', 'natural']. The 2 special ones are 'none' and 'natural' which can't be specified with anything else because 'none' dumps everything in the group_folder_path (so no folder nesting can be specified) and 'natural' specifies ['cond', 'XY'] because they you can see images by condition then by capture point (if you have multiple capture points in the same well).

--ypath yaml_path: The path to where the yaml file is that specifies the well conditions. If no yaml_path is given, kfm will look in the group_folder_path. Conditions must be specified as an array called wells. Here is an example yaml file:

2021.08.19_key.yaml

wells:
  - NIL: A1-C4
  - DD: B1-C4
  - RR: C1-C4
  - puro_ctrl: D1 

Conditions can be overlaid over each other. In the above example, wells A1-A4 are just NIL, but wells B1-B4 are NIL_DD. This make it easy to overlay several conditions in the same well. In addition, single wells can be specified, such as in the example of D1 and puro_ctrl. This would result in something like this after kfm was used.

.
├── 2021.08.12_NT_reprogram_4dpi
    ├── NIL
    ├── NIL.DD
    ├── NIL.DD.RR
    ├── puro_ctrl
    ├── record.json
    └── unmoved

The yaml file can be called anything, as long as it ends in .yaml and is found within the yaml_path. yaml_path can be the directory where the yaml file is or the actual file name. In the case where it's the directory, kfm will use the first .yaml file that it finds.

yaml examples

yaml files can be named different things, as long as it ends in the correct .yaml extension. Here's another example of a well specification yaml file:

key.yaml

# path: '/Users/Nathan/OneDrive - Massachusetts Institute of Technology/Documents - GallowayLab/instruments/data \
#        /keyence/Nathan/Degron-mGL/2021.07.29_293T_2dpt'

wells:
  - pMXs-mGL: A1-A4
  - pMXs-mGL-MODC: B1-B4
  - pMXs-mGL-MODC_mut: C1-C4
  - pMXs-mGL-Ubi-Y-dK: D1-D4
  - pMXs-mGL-UbR: E1-E4
  - pMXs-eGFP-WPRE: F1-F4
  - pMXs-eGFP-MODC: G1-G4

For yaml file naming, the command:

$ kfm ./Degron-mGL/2021.07.29_293T_2dpt

would work on the following yaml files:

1. ./Degron-mGL/2021.07.29_293T_2dpt/key.yaml
2. ./Degron-mGL/2021.07.29_293T_2dpt/2021.07.29_key.yaml

Because no yaml path is specified using the --ypath yaml_path arg, kfm will look in the specified group_folder_path. But the following command would only work with the first example because a specific yaml file is specified instead of a general directory to look into:

$ kfm ./Degron-mGL/2021.07.29_293T_2dpt/key.yaml

The optional --ypath arg is useful to reorganize multiple group folders that have the same well layout (e.g. for biological replicates). For example, the following 3 folders could be quickly reorganized with following 3 commands:

.
├── Degron-mGL
    ├── 2021.07.29_293T_2dpt_01
    ├── 2021.07.30_293T_2dpt_02
    ├── 2021.07.31_293T_2dpt_03
    └── key.yaml

$ kfm ./Degron-mGL/2021.07.29_293T_2dpt_01 --ypath ./Degron-mGL/

$ kfm ./Degron-mGL/2021.07.30_293T_2dpt_02 --ypath ./Degron-mGL/

$ kfm ./Degron-mGL/2021.07.31_293T_2dpt_03 --ypath ./Degron-mGL/

Developer install

If you'd like to hack locally on kfm, after cloning this repository:

$ git clone https://github.com/GallowayLabMIT/kfm.git
$ cd git

you can create a local virtual environment, and install kfm in "development mode"

$ python -m venv env
$ .\env\Scripts\activate    (on Windows)
$ source env/bin/activate   (on Mac/Linux)
$ pip install -e .

After this 'local install', you can use kfm freely, and it will update in real time as you work.

License

This is licensed by the MIT license. Use freely!