BIO407 Group3 Image processing of live cells, treated with DFX

## Study:
This data is part of the practical course BIO407 2025 at the University of Zurich, titled 'Advanced Microscopy: From preparation to data and visualization'.
The effects of Deferasirox (DFX) on mitochondria morphology were examined using different microscopy techniques.
The data is originally from the paper:
Gottwald EM, Schuh CD, Dr點ker P, Haenni D, Pearson A, Ghazi S, Bugarski M, Polesel M, Duss M, Landau EM, Kaech A, Ziegler U, Lundby AKM, Lundby C, Dittrich PS, Hall AM. The iron chelator Deferasirox causes severe mitochondrial swelling without depolarization due to a specific effect on inner membrane permeability. Sci Rep. 2020 Jan 31;10(1):1577. doi: 10.1038/s41598-020-58386-9. PMID: 32005861; PMCID: PMC6994599.

## Study Component:
Job: Image Processing
Task: 4) Timelapse of mitochondria in deferasirox (DFX) treated cells
Timelapse data was analyzed: Mitochondria were segmented, their morphology and signal intensity were measured over time, and plotted.

## Biosample:
Opossum kidney (OK) cells (kind gift from the group of Prof O. Devuyst (Physiology, University of Zurich))

## Specimen:
DFX treatment: 200uM
Dyes:
-Mitochondria-GFP BacMam 2.0
-TMRM (mitochondrial membrane potential dependent dye)

## Image Acquisition:
Images were acquired using a Leica SP8 inverse STED 3x.
Acquired channels:
Channel 1: Mitochondria-GFP, 488nm excitation, 493nm-548nm emission
Channel 2: TMRM, 553nm excitation, 564nm-650nm emission
Objective: HC PL APO CS2 100x/1.40 OIL

## Image Data:
Raw timelapse data:
    Raw data dataset 5 > 151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression.lif
Segmentation masks of mitochondria:
    Segmetation mask.tif
documentation of the analysis steps:
    Analysis process.txt
Measurements of segmented mitochondria at different timepoints:
    Measurements.csv
Plot of mean mitochondria circularity over time:
    Mitochondria circularity plot.png
Plot of mean GFP signal in mitochondria over time:
    Mitochondria mean signal intensity plot.png
Plot of segmented mitochondria count over time:
    Mitochondria count plot.png

## Image Correlation
Segmentation mask.tif contains the segmentation masks for the timelapse in 151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression.lif
Measurements.csv contains the measurements gotten by applying the steps described in Analysis process.txt the raw data file 151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression.lif
all plots were generated from the Measurements.csv data

## Image Analysis
See Analysis process.txt