Microscopy image sequences and annotated kymographs of laser ablation experiments in Drosophila embryos
DOI10.5281/zenodo.3257654Zenodo3257654MaRDI QIDQ6698655FDOQ6698655
Dataset published at Zenodo repository.
Bénédicte Sanson, Elena Scarpa, Nilankur Dutta, Carola-Bibiane Schönlieb, Lukas F. Lang, Jocelyn Étienne
Publication date: 30 June 2019
Copyright license: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
Content Thisdataset contains 15 2Dtime-lapse fluorescence microscopy image sequences recorded withconfocal laser-scanning microscopy. Each movieshows an epithelialtissue laser nanoablation experiment conducted in a Drosophila embryo. For each sequence, the datasetcontains kymographs (one-dimensional space-time plots) of asupracellularcable that is cut during the ablation, and manually created tracks of visible features, such as the resulting cut ends. These tracks allow to estimate, for instance, recoil velocities of the cut tissue and may be used to evaluate automated methods for estimating said velocities. Thisdataset is used in the manuscript to evaluate various variational approaches for joint motion estimation and source identification: L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schnlieb, and J. Étienne. Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations.2019. Description The moviesdepict a square region of approximately\(42.2 \times 42.2 \, \mathrm{\mu m}^{2}\) at a spatial resolution of \(250 \times 250\)pixels. A typical sequence contains between 60 and 100 frames. Theytemporal interval between recorded frames was\(727.67 \, \mathrm{ms}\). Each sequence features cell membranes labelled withE-cadherin:GFP and showsasingle plasma-induced laser nanoablation. The destructed tissueregion is roughly of\(2 \, \mathrm{\mu m}\)length. This ablation is expected to have a width of the order of the size of one pixel. During the ablation the acquisition is paused, resulting in a black image. For the used microscopy techniques and for the preparation of flies, as well as for the details of the laser ablation method, seethe paper: E. Scarpa, C. Finet, G. B. Blanchard, and B. Sanson. Actomyosin-driven tension at compartmental boundaries orients cell division independently of cell geometry In Vivo. Dev. Cell, 47(6):727740.e6, December 2018. URL:https://doi.org/10.1016/j.devcel.2018.10.029 The kymographs and the manually created annotations (tracks)of featureswerecreated usingFiji (https://fiji.sc/). Content The dataset contains 15 sequences placed in the following folder structure: SqAX3_SqhGFP42_GAP43_TM6B 190216E4PSB1 190216E5PSB1 190216E5PSB2 190216E6PSB1 190216E8PSB1 E2PSB1 E5PSB2 E8PSB1 PSB1E1 PSB4 SqhGFP40 e1_PSB8 e3_PSB9 e3_PSB10 e4_PSB11 e4_PSB12 Each folder contains: The sequence itselfin TIF format, e.g. 190216E4PSB1PMT - PMT [560-] _C1.ome.tif. A file reslice.roi thatindicates the location/direction of the cut supracellular cable. 3 different kymographs for each sequence obtained by taking avg/max/sum projections in Fijiorthogonal tothe line specified inreslice.roi, e.g. AVG_Reslice of 190216E4PSB1PMT.tif, MAX_Reslice of 190216E4PSB1PMT.tif, SUM_Reslice of 190216E4PSB1PMT.tif. Text files that state the time/space coordinates of manually tracked features in the kymographs, e.g. cutend_L.txt (coordinates of theleft cut end after the ablation), cutend_R.txt (coordiantes of the right cut end), feat_X.txt (coordinates of additional features, where X is a number and L or R). A ZIP filemanual_ROIs.zip that contains all the coordinates of tracked features of the kymographin ROI format (e.g. cutend_L.roi). Usage The sequences, kymographs, and the trackscan be viewed using, for example,Fiji. For theautomated analysis,see the Python code that accompanies the manuscript above. It is available athttps://dx.doi.org/XXX License information This dataset is released underCreative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. SeeCC BY-NA-SC 4.0. How to cite this dataset If you use this dataset in an academic publication, please consider citingthe paper: L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schnlieb, and J. Étienne. Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations.2019. To cite solelythe dataset, please use: L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schnlieb, and J. Étienne. (2019). Microscopy image sequences and annotated kymographs of laser ablation experiments in Drosophila embryos [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3257654
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