Phriction Projects Wikis Bioimaging And Optics Platform Image Processing BIOP GISTS History Version 6 vs 7
Version 6 vs 7
Version 6 vs 7
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Content Changes
This aims to be an exhaustive list of Gists that are of relevance to the BIOP and that were produced by us
|Name|Description|Author|Tags|Date|
|----|-----------|------|----|----|
| **[[ https://gist.github.com/be7cfba6ba1d26594598|ColocExamples.m ]]** | Using the Coloc Function in EasyXT | Olivier Burri | `#Imaris`, `#EasyXT`, `#Coloc`, `#Matlab`, `#BIOP` | 2020/10/22 |
| **[[ https://gist.github.com/a2d19870e5e74140b0c1c9576a8b89da|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 |
| **[[ https://gist.github.com/d284ef91160f9242ab8ce3a65b72cbd6|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` | 2020/10/22 |
| **[[ https://gist.github.com/16e12482b52f539795e49cb2122060cc|Export_Images_Folder.ijm ]]** | Extract multi-series file and resave as TIFF stacks or slices | Olivier Burri | `#Fiji`, `#ImageJ`, `#Macro`, `#BIOP` | 2020/10/22 |
| **[[ https://gist.github.com/f99287e4b0fcc6ac9bc07a946a867bb0|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 |
| **[[ https://gist.github.com/640b4a3a1f6e786114702c904473933d|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 |
| **[[ https://gist.github.com/a005c15c6a8735d7d904e85b9663b82d|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 |
| **[[ https://gist.github.com/0a12113b1497db86d7df3ef102efd34d|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 |
| **[[ https://gist.github.com/f20223c199a33d628cbc0e196fa0b045|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 |
This aims to be an exhaustive list of Gists that are of relevance to the BIOP and that were produced by us
|Name|Description|Author|Tags|Date|
|----|-----------|------|----|----|
| **[[ https://gist.github.com/4c9d795fe21df30c356efccaa4942043|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 |
| **[[ https://gist.github.com/9e0dee82690bcfa670edeadb7fdcae0a|BIOP-userProject.ijm ]]** | A ImageJ macro to create a standardized "User Project" folder. | Romain Guiet | `#BIOP`, `#FIJI`, `#Macro`, `#UserProject` | 2020/10/29 |
| **[[ https://gist.github.com/8b59a90ad87e7c6a1af26194a45cd181|closeOthers.groovy ]]** | groovy command equivalent to 'close("\\others")' in macro language. | Romain Guiet | `#BIOP`, `#Groovy`, `#Macro` | 2020/10/30 |
| **[[ https://gist.github.com/be7cfba6ba1d26594598|ColocExamples.m ]]** | Using the Coloc Function in EasyXT | Olivier Burri | `#Imaris`, `#EasyXT`, `#Coloc`, `#Matlab`, `#BIOP` | 2020/10/22 |
| **[[ https://gist.github.com/a2d19870e5e74140b0c1c9576a8b89da|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 |
| **[[ https://gist.github.com/d284ef91160f9242ab8ce3a65b72cbd6|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 |
| **[[ https://gist.github.com/16e12482b52f539795e49cb2122060cc|Export_Images_Folder.ijm ]]** | Extract multi-series file and resave as TIFF stacks or slices | Olivier Burri | `#Fiji`, `#ImageJ`, `#Macro`, `#BIOP` | 2020/10/22 |
| **[[ https://gist.github.com/3dc23527406205b36c41b1baf41240cc|Find_FalsePositive_threshold.ijm ]]** | An ImageJ macro to determine False Positive threshold on control images. | Romain Guiet | `#BIOP`, `#FIJI`, `#Macro`, `#Coloc` | 2020/10/29 |
| **[[ https://gist.github.com/f99287e4b0fcc6ac9bc07a946a867bb0|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 |
| **[[ https://gist.github.com/45f865b5a38d7c3a96a7cd8b25923407|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 |
| **[[ https://gist.github.com/435806a12e548ec1adcc2af1eff1002a|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 |
| **[[ https://gist.github.com/b266251d90679de3bc6fdda3cc61d5f9|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 |
| **[[ https://gist.github.com/5dfee7977e27bdf695cbf4f0b2c3cb8a|Lazy_3DAnnotations.ijm ]]** | ij macro prototype for lazy 3D annotations reyling on ROIs interpolation. | Romain Guiet | `#BIOP`, `#FIJI`, `#Annotations`, `#Labels` | 2020/10/29 |
| **[[ https://gist.github.com/640b4a3a1f6e786114702c904473933d|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 |
| **[[ https://gist.github.com/a005c15c6a8735d7d904e85b9663b82d|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 |
| **[[ https://gist.github.com/6f70f60e98fa3e44fa23f1d85c303c82|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 |
| **[[ https://gist.github.com/0a12113b1497db86d7df3ef102efd34d|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 |
| **[[ https://gist.github.com/f20223c199a33d628cbc0e196fa0b045|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 |
This aims to be an exhaustive list of Gists that are of relevance to the BIOP and that were produced by us
|Name|Description|Author|Tags|Date|
|----|-----------|------|----|----|
| **[[ https://gist.github.com/4c9d795fe21df30c356efccaa4942043|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 |
| **[[ https://gist.github.com/9e0dee82690bcfa670edeadb7fdcae0a|BIOP-userProject.ijm ]]** | A ImageJ macro to create a standardized "User Project" folder. | Romain Guiet | `#BIOP`, `#FIJI`, `#Macro`, `#UserProject` | 2020/10/29 |
| **[[ https://gist.github.com/8b59a90ad87e7c6a1af26194a45cd181|closeOthers.groovy ]]** | groovy command equivalent to 'close("\\others")' in macro language. | Romain Guiet | `#BIOP`, `#Groovy`, `#Macro` | 2020/10/30 |
| **[[ https://gist.github.com/be7cfba6ba1d26594598|ColocExamples.m ]]** | Using the Coloc Function in EasyXT | Olivier Burri | `#Imaris`, `#EasyXT`, `#Coloc`, `#Matlab`, `#BIOP` | 2020/10/22 |
| **[[ https://gist.github.com/a2d19870e5e74140b0c1c9576a8b89da|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 |
| **[[ https://gist.github.com/d284ef91160f9242ab8ce3a65b72cbd6|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` | 2020/10/22 |1/15 |
| **[[ https://gist.github.com/16e12482b52f539795e49cb2122060cc|Export_Images_Folder.ijm ]]** | Extract multi-series file and resave as TIFF stacks or slices | Olivier Burri | `#Fiji`, `#ImageJ`, `#Macro`, `#BIOP` | 2020/10/22 |
| **[[ https://gist.github.com/3dc23527406205b36c41b1baf41240cc|Find_FalsePositive_threshold.ijm ]]** | An ImageJ macro to determine False Positive threshold on control images. | Romain Guiet | `#BIOP`, `#FIJI`, `#Macro`, `#Coloc` | 2020/10/29 |
| **[[ https://gist.github.com/f99287e4b0fcc6ac9bc07a946a867bb0|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 |
| **[[ https://gist.github.com/45f865b5a38d7c3a96a7cd8b25923407|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 |
| **[[ https://gist.github.com/435806a12e548ec1adcc2af1eff1002a|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 |
| **[[ https://gist.github.com/b266251d90679de3bc6fdda3cc61d5f9|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 |
| **[[ https://gist.github.com/5dfee7977e27bdf695cbf4f0b2c3cb8a|Lazy_3DAnnotations.ijm ]]** | ij macro prototype for lazy 3D annotations reyling on ROIs interpolation. | Romain Guiet | `#BIOP`, `#FIJI`, `#Annotations`, `#Labels` | 2020/10/29 |
| **[[ https://gist.github.com/640b4a3a1f6e786114702c904473933d|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 |
| **[[ https://gist.github.com/a005c15c6a8735d7d904e85b9663b82d|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 |
| **[[ https://gist.github.com/0a12113b1497db86d7df3ef102efd34d|Prune_Skeleton_Ends.bsh ]]** | [Prune Skeleton Ends] Script to prune skeletons endpoints whose branches are shorter than the specified distan6f70f60e98fa3e44fa23f1d85c303c82|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 | `#Beanshell`, `#ImageJ``#fiji`, `#Fiji``#imageJ`, `#Skeleton``#histogram`, `#BIOP` | 2020/10/22 |1/03 |
| **[[ https://gist.github.com/f20223c199a33d628cbc0e196fa0b045|Pseudo_3D_Gaussian_Fit_Using_Reslice.ijm ]]** | Reslices a dataset0a12113b1497db86d7df3ef102efd34d|Prune_Skeleton_Ends.bsh ]]** | [Prune Skeleton Ends] Script to prune skeletons endpoints whose branches are shorter than the specified distance | Olivier Burri | `#Beanshell`, fits gaussians in 2D before performing a 1D fit in Z | Olivier Burri | `#ImageJ`, `#Macro``#Fiji`, `#Fiji``#Skeleton`, `#BIOP` | 2020/10/22 |
| **[[ https://gist.github.com/f20223c199a33d628cbc0e196fa0b045|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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