Sample Experiments

We provide some partial data from three experiments performed in the Siegal lab, and sample setup files that can be used to analyze them.

Downloading example experiments

If you downloaded the full PIE github repository, you can find the sample experiments in the PIE_test_data/IN/ directory, and the sample setup files in sample_PIE_setup_files/.

If you do not want to download the full github repository, you can use DownGit to selectively download these two folders:

After downloading the folders, you will need to unzip them.

Note

The rest of the code assumes that you have PIE installed, and that you are in a directory that contains both the unzipped PIE_test_data/ and sample_PIE_setup_files/ folders.

Any outputs will be created inside PIE_test_data/out/

Example data

Single-phase growth rate experiment

Experiment PIE_test_data/IN/SL_170619_2_GR_small contains a subset of the Saccharomyces cerevisiae data described in Figure 5 of the PIE paper. It is a growth rate experiment that originally had 4032 fields imaged at 10 timepoints; partial images from a small subset of fields is included here. This experiment can be analyzed using either sample_PIE_setup_files/gr_phase_setup_simple.csv, or sample_PIE_setup_files/gr_phase_setup.csv; the latter includes advanced options and filtration settings closer to those typically used for analysis in our lab.

pie run_timelapse_analysis sample_PIE_setup_files/gr_phase_setup.csv

Growth rate experiment with post-phase fluorescence

Experiment PIE_test_data/IN/EP_170202_small contains a subset of the data from a Saccharomyces cerevisiae growth rate experiment that originally had 4032 fields imaged at 10 timepoints (located in PIE_test_data/IN/EP_170202_small/EP_170202_2_GR), plus an additional post-growth-phase, fluorescent-only set of images in the GFP channel (located in PIE_test_data/IN/EP_170202_small/EP_170202_2_FC). Each imaging position includes cells from two strains, one of which is expressing GFP driven by the Scw11 promoter; GFP levels can therefore be used to differentiate between these strains, and setting the first phase of the experiment as the ‘linked’ phase for the fluorescence imaging will automatically trigger fluorescence-based classification of each colony.

Note also that here, the brightfield images are saved as .jpg files; while not ideal, PIE can still process these images.

This experiment can be analyzed using either sample_PIE_setup_files/gr_with_postfluor_setup_simple.csv or sample_PIE_setup_files/gr_with_postfluor_setup.csv; the latter includes advanced options and filtration settings closer to those typically used for analysis in our lab.

pie run_timelapse_analysis sample_PIE_setup_files/gr_with_postfluor_setup.csv

Two-phase growth rate experiment with simultaneous fluorescence measurement

Experiment PIE_test_data/IN/SL_180519_small contains a subset of the data from a Saccharomyces cerevisiae growth rate experiment from Figure 9 in Li *et al.* 2018. The experiment initially consisted of 1200 imaging fields that were imaged over two phases before and after a heat shock: five timepoints of pre-heat shock growth rate (located in PIE_test_data/IN/SL_180519_small/SL_180519_2_GR) and fifteen timepoints post-heat shock (located in PIE_test_data/IN/SL_180519_small/SL_180519_2_AT). Fluorescent data was also collected at each timepoint during both phases: detecting MitoTracker staining and Tsl1-GFP expression in the first phase, and only Tsl1-GFP in the second phase.

An analysis of just the first phase of the experiment (including fluorescence data) can be used to explore the output of PIE for combined growth/fluorecence experiments using sample_PIE_setup_files/gr_with_fluor_setup_simple.csv

pie run_timelapse_analysis sample_PIE_setup_files/gr_with_fluor_setup_simple.csv

The full experiment can be analyzed using either sample_PIE_setup_files/two_phase_setup_simple.csv, or sample_PIE_setup_files/two_phase_setup.csv; the latter includes advanced options and filtration settings closer to those typically used for analysis in our lab. Note that these setup files are set up to exclude images for the first two time points after heat shock from the analysis, as heat-induced warping causes colonies to be out of focus during these time points.

pie run_timelapse_analysis sample_PIE_setup_files/two_phase_setup.csv