This scripts takes as an input a Google Drive folder in which tempora metrological data from several microscopes have been stored and builds XLSX and PPTX reports from the data. Data should have been exported using the Fiji/ImageJ MetroloJ plugin, along side the power measurements that have been properly formatted. The following section gives information about what data structure is expected.
Microscope 1 (subfolder)
Power_file (mandatory, see below for a full description)
YYMMDD (subfolder, date at which measurement was done: should match dates in the power_file)
pdf (optionnal subfolder, stores the pdf extracted by the MetroloJ plugin)
table (mandatory subfolder, stores tables extracted by the MetroloJ plugin)
YYMMDD (subfolder, date at which measurement was done: should match dates in the power_file)
pdf (optionnal subfolder, stores the pdf extracted by the MetroloJ plugin)
table (mandatory subfolder, stores tables extracted by the MetroloJ plugin)
Microscope 2 (subfolder)
Power_file (mandatory, see below for a full description)
YYMMDD (subfolder, date at which measurement was done: should match dates in the power_file)
pdf (optionnal subfolder, stores the pdf extracted by the MetroloJ plugin)
table (mandatory subfolder, stores tables extracted by the MetroloJ plugin)
YYMMDD (subfolder, date at which measurement was done: should match dates in the power_file)
pdf (optionnal subfolder, stores the pdf extracted by the MetroloJ plugin)
table (mandatory subfolder, stores tables extracted by the MetroloJ plugin)
The powers file contains all measured powers as tabulation separated values.
The filename should be puissance.csv.
There is only one puissance.csv file per microscope folder, stored at its root.
The file is assumed to contain the following columns:
- date: should be formatted as YYMMDD, not forgetting the leading zeros
- source: name of the light source (LED, laser etc)
- obj: objective that was used for measurements
- Channel_405: illumination setting used for measuring the 405 channel
- Channel_488: illumination setting used for measuring the 488 channel
- Channel_561: illumination setting used for measuring the 561 channel
- Channel_633: illumination setting used for measuring the 633 channel
- 405: power measured using the Channel 405 illumination setting (in mW)
- 488: power measured using the Channel 488 illumination setting (in mW)
- 561: power measured using the Channel 561 illumination setting (in mW)
- 633: power measured using the Channel 633 illumination setting (in mW)
Data are stored, one date per line
ex:
date source obj Channel_405 Channel_488 Channel_561 Channel_633 405 488 561 633
201201 LED 10x 0 Eye-GFP_50pct 0 0 0.000 18.800 0.000 0.000
201218 LED 10x Eye-DAPI_50pct Eye-GFP_50pct Eye-TRITC_50pct Fluo - CY5 quad quad 51.300 17.300 16.470 11.170
210127 LED 10x Eye-DAPI_50pct Eye-GFP_50pct Eye-TRITC_50pct Fluo - CY5 quad quad 43.5 15.12 14.96 9.17
- Upload this script to Google Colab using the dedicated button
- Once in Google Colab, first go to File/Save a copy to my Google Drive
- Have all you data ready on the Google Drive
- Run all the steps: Run/Run all
- Step 1 only is interactive: it will require that acces is given by the Google Drive to the script. Simply follow the procedure explained at Step 1.1
- The metrology root folder should be defined: follow the procedure explained at Step 1.2
- All subsequent steps are run without any interaction with the user
- At the end of the script, two files are generated in the metrology root folder:
- An XLSX file containing all the data pulled into a single, multitabs file
- A PPTX file containing graphs for all microscopes/dates/measurements