BIOP GISTS
BIOP GISTS
This aims to be an exhaustive list of Gists that are of relevance to the BIOP and that were produced by us.
Updating this document with newly created gists is as simple as launching binder from the repo : https://github.com/BIOP/gist-query
| Name | Description | Author | Tags | Date |
|---|---|---|---|---|
| BIOP-DiAna.ijm | An example ImageJ macro language script to run DiAna (images available here : https://drive.switch.ch/index.php/s/nfVRYJIic3lsfhm , supporting slides here : https://go.epfl.ch/2020-intro-diana ) | Romain Guiet | #BIOP, #Fiji, #Coloc, #DiAna | 2020/10/29 |
| BIOP-userProject.ijm | A ImageJ macro to create a standardized "User Project" folder. | Romain Guiet | #BIOP, #FIJI, #Macro, #UserProject | 2020/10/29 |
| closeOthers.groovy | groovy command equivalent to 'close("\\others")' in macro language. | Romain Guiet | #BIOP, #Groovy, #Macro | 2020/10/30 |
| ColocExamples.m | Using the Coloc Function in EasyXT | Olivier Burri | #Imaris, #EasyXT, #Coloc, #Matlab, #BIOP | 2020/10/22 |
| DisplayRoisInBdv.groovy | [Display ROIs in BigDataViewer] Display ROIs of the RoiManager linked to an ImagePlus using BigDataViewer ( ImageJ / FIJI ) | Nicolas Chiaruttini | #Fiji, #ROI, #BigDataViewer, #BIOP | 2020/10/26 |
| Export Annotations For Stardist.groovy | [QuPath Script To Export Annotations For Stardist] this script will take rectangular annotations in QuPath and export them and their containing objects as images and masks for deep neural netowrk training | Olivier Burri | #qupath, #stardist, #BIOP | 2020/11/15 |
| Export_Images_Folder.ijm | Extract multi-series file and resave as TIFF stacks or slices | Olivier Burri | #Fiji, #ImageJ, #Macro, #BIOP | 2020/10/22 |
| Find_FalsePositive_threshold.ijm | An ImageJ macro to determine False Positive threshold on control images. | Romain Guiet | #BIOP, #FIJI, #Macro, #Coloc | 2020/10/29 |
| FlatField_And_Stitch.groovy | [Flatfield correction followed by stitching] Performs a flatfield correction and stitching from Raw LIF, CZI and LSM files using plugins in Fiji | Olivier Burri | #Fiji, #Stitching, #Groovy, #Flatfield, #LIF, #LSM, #CZI, #BIOP | 2020/10/22 |
| FWHM.ijm | [1D Full Width At Half Maximum] This computes the Full Width at Half Maximum FWHM in an image for anz line profile drawn on the image and added to the ROI manager | Olivier Burri | #fiji, #imageJ, #BIOP, #FWHM | 2020/11/03 |
| IJMeasureLifeTimeBasic.ijm | [Simple Life Time Measurement in ImageJ] Estimate lifetime of ROIs based on single exponential fits ( ImageJ / FIJI ) | Nicolas Chiaruttini | #Fiji, #ROI, #FLIM, #BIOP | 2020/11/23 |
| ijs-export_lif_zprojAvailable.groovy | A groovy script usable in FIJI to export images of a lif file (should work with other bioformats supported format). User can specify the series to export using comma (1,2,3) or a range using dash (1-5) , or nothing to export all series | Romain Guiet | #BIOP, #FIJI, #groovy, #export, #bioformats | 2020/11/09 |
| ilastik4fiji.ijm | a minimal example of ilastik called from fiji. https://go.epfl.ch/ilastik-tuto-2020 | Romain Guiet | #BIOP, #fiji, #macro, #ilastik | 2020/11/06 |
| image_and_pointList_toXML.ijm | Romain Guiet | #macro, #xml, #LabelImg, #ZeroCostDL4Mic, #BIOP | 2020/11/18 | |
| Lazy_3DAnnotations.ijm | ij macro prototype for lazy 3D annotations reyling on ROIs interpolation. | Romain Guiet | #BIOP, #FIJI, #Annotations, #Labels | 2020/10/29 |
| Local_Thickness_Parallel.groovy | [Run Fiji Local Thickness in Parallel] this script can crop blob-like objects in an image using Find Maxima and runs Local Thickness on each cropped image. | Olivier Burri | #fiji, #imagej, #imagesc, #localthickness, #BIOP | 2020/10/22 |
| Normalize_Line_Straighten.ijm | [Nomalize Line Profile] Normalizes line profiles by making use of the Straighten command followed by scaling | Olivier Burri | #Macro, #ImageJ, #Fiji, #BIOP | 2020/10/22 |
| Parallel_HistrogramEqualize_All_Slices | [Parallel Histrogram-Based Normalization] This performs Histogram Based Normalization on all slices of an open stack based on the selected reference slice | Olivier Burri | #fiji, #imageJ, #histogram, #BIOP | 2020/11/03 |
| Prune_Skeleton_Ends.bsh | [Prune Skeleton Ends] Script to prune skeletons endpoints whose branches are shorter than the specified distance | Olivier Burri | #Beanshell, #ImageJ, #Fiji, #Skeleton, #BIOP | 2020/10/22 |
| Pseudo_3D_Gaussian_Fit_Using_Reslice.ijm | Reslices a dataset, fits gaussians in 2D before performing a 1D fit in Z | Olivier Burri | #ImageJ, #Macro, #Fiji, #BIOP | 2020/10/22 |
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- Last Author
- chiarutt
- Last Edited
- Nov 23 2020, 17:59