DOI: 10.5281/zenodo.14979239
title: BIO407 Group4 Image processing of live cells, treated with DFX

description: ## 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:

151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression.lif

Metadata of raw timelapse data:

metadata_raw_data.txt

Segmentation masks of mitochondria:

GFP: 151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression_Mask_Channel1.tif

TMRM: 151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression_Mask_Channel2.tif

FIJI macro, documenting the analysis steps:

Fiji_analysis.ijm

Mean circularity of segmented mitochondria at each timepoint measured with GFP signal (Circ.) and Mean GFP signal intensity of segmented mitochondria at each timepoint (Mean): 

Channel1_Measurements.csv

Mean circularity of segmented mitochondria at each timepoint measured with TMRM signal (Circ.) and Mean TMRM signal intensity of segmented mitochondria at each timepoint (Mean): 

Channel2_Measurements.csv

Plot of mean mitochondria circularity over time:

GFP: Channel1_Circularity.png

TMRM: Channel2_Circularity.png

Plot of mean GFP signal in mitochondria over time:

Channel1_MeanIntensity.png

Plot of mean TMRM signal in mitochondria over time:

Channel2_MeanIntensity.png

 

## Image Correlation

 

151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression_Mask_Channel1.tif

and

151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression_Mask_Channel2.tif

contain the segmentation masks for the timelapse in 151106_slide1_bacmam20_PPC_7473_Esther_DH_Progression.lif

 

## Image Analysis

 

We used FIJI to perform a segmentation of the mitochondria. Individual steps can be found in the FIJI Macro. (Fiji_analysis.ijm) 

The segmentation masks were analyzed in FIJI and the 'Analyze Particles' command was used to measure the circularity and mean signal intensity of all segmented mitochondria. The mean measurements were then plotted for each timepoint.