Phriction Projects Wikis Bioimaging And Optics Platform Image Processing BIOP GISTS History Version 4 vs 5
Version 4 vs 5
Version 4 vs 5
Content Changes
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/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/be7cfba6ba1d26594598|ColocExamples.m ]]** | Using the Coloc Function in EasyXT | Olivier Burri | `#Imaris`, `#EasyXT`, `#Coloc`, `#Matlab`, `#BIOP` | 2020/10/22 |
| **[[ 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/be7cfba6ba1d26594598|ColocExamples.m ]]** | Using the Coloc Function in EasyXT | Olivier Burri | `#Imaris`, `#EasyXT`, `#Coloc`, `#Matlab`, `#BIOP` | 2020/10/22 |
| **[[ 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 |
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