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|
|----|-----------|------|----|----|
| **[[ https://gist.github.com/15e8d39d4d18174a22402c2ca939bb81|bf2ometiff.groovy ]]** | Batch conversion to pyramidal ome-tiff using Glencoe Software optimized workflow | Nicolas Chiaruttini | `#BIOP`, `#Fiji`, `#OmeTiff`, `#MRXS` | 2022/01/26 |
| **[[ 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` | 2022/03/18 |
| **[[ https://gist.github.com/9e0dee82690bcfa670edeadb7fdcae0a|BIOP-userProject.ijm ]]** | A ImageJ macro to create a standardized "User Project" folder. | Romain Guiet | `#BIOP`, `#FIJI`, `#Macro`, `#UserProject` | 2021/06/16 |
| **[[ https://gist.github.com/ec7022acf1967e89e14880a7b8b7d911|checkUpdateSites.groovy ]]** | How to investigate the list of Update Sites enabled | Nicolas Chiaruttini | `#BIOP`, `#Fiji`, `#UpdateSites` | 2022/01/14 |
| **[[ 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/1efa49eb23b2438a603ea1f531be77bd|DendritesAnalysis.groovy ]]** | [Spine analysis] Analyse and output cropped images around each spine. Needs a Simple Neurite Tracer input - | Nicolas Chiaruttini | `#BIOP`, `#Fiji`, `#SNT` | 2020/12/18 |
| **[[ https://gist.github.com/f45f56e3ff2d1fb708821c110fbdee62|DetectCellsABBA.groovy ]]** | Performs cell detection in QuPath from an ABBA registered project with imported regions | Nicolas Chiaruttini | `#BIOP`, `#ABBA`, `#QuPath` | 2022/02/08 |
| **[[ 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` | 2020/11/30 |
| **[[ 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` | 2021/05/24 |
| **[[ https://gist.github.com/cb2eaba47ad001c49b7c232dc6313de9|Export Contiguous Fields.groovy ]]** | [Operetta Export Contiguous Fields] Uses Flood filling on the fields to find which ones are direct neighbors and exports each as a separate ImagePlus. Example | Olivier Burri | `#Operetta`, `#Fiji`, `#Groovy`, `#BIOP` | 2021/07/15 |
| **[[ 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` | 2022/01/25 |
| **[[ https://gist.github.com/9458c7342d3d6651a6e8c279a68c85bd|ExportCellDataABBA.groovy ]]** | Export Cell Data from an ABBA registered project | Nicolas Chiaruttini | `#BIOP`, `#ABBA`, `#QuPath` | 2022/02/08 |
| **[[ https://gist.github.com/142258b2eef49e3bb1bb5b0309c81e00|FijiMultiSeriesExporter.groovy ]]** | Takes a bioformats compatible file and batch exports individual series, optionally Z Projected and rescaled | Nicolas Chiaruttini | `#BIOP`, `#Fiji`, `#BigDataViewer` | 2022/03/29 |
| **[[ 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` | 2021/08/18 |
| **[[ https://gist.github.com/5df8c91bc296ad52526b8db6b3548dea|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 |
| **[[ https://gist.github.com/08e60992a286d7c3e44ad9f453ff0d0a|ijs-EasyXT-Filter_detectedSpots.groovy ]]** | An example script to show how to filter spots after the detection. | Romain Guiet | `#Fiji`, `#EasyXT-Fiji`, `#Imaris`, `#BIOP` | 2020/12/18 |
| **[[ 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/288dfec7fc2534fe7af027f88a971f9b|image_and_pointList_toXML.ijm ]]** | | Romain Guiet | `#macro`, `#xml`, `#LabelImg`, `#ZeroCostDL4Mic`, `#BIOP` | 2020/11/18 |
| **[[ https://gist.github.com/723d8e628a3bb03902bb3f0f2f0fa466|ImportABBARegions.groovy ]]** | Import Atlas regions in QuPath from an ABBA registered project | Nicolas Chiaruttini | `#BIOP`, `#ABBA`, `#QuPath` | 2022/02/08 |
| **[[ 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/558b26558260a3de96348996ac50d674|NikonStereologyBdvVisualizer.groovy ]]** | Takes a Nikon ND2 file and visualizes it lazily in BigDataViewer | Nicolas Chiaruttini | `#BIOP`, `#Fiji`, `#BigDataViewer`, `#NikonStereology` | 2021/03/29 |
| **[[ https://gist.github.com/d08618d3b8b04bafe0ab9520c59edf5e|NikonStereologyExporter.groovy ]]** | Takes a Nikon ND2 file and batch exports individual series, optionally Z Projected and rescaled | Nicolas Chiaruttini | `#BIOP`, `#Fiji`, `#BigDataViewer`, `#NikonStereology` | 2021/03/29 |
| **[[ 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.groovy ]]** | [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` | 2021/06/02 |
| **[[ 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/ca52778d11870043e04daff5f5afb75c|RecursiFIJI.groovy ]]** | | Nicolas Chiaruttini | `#BIOP`, `#BigDataViewer` | 2021/06/22 |
| **[[ https://gist.github.com/25369ed257d1be68554f7da3023da52c|RemoveABBARegions.groovy ]]** | Re-import ABBA regions then filter out regions based on name | Nicolas Chiaruttini | `#BIOP`, `#ABBA`, `#QuPath` | 2022/02/10 |
| **[[ https://gist.github.com/ae1f598e734d563083eddad90ee17e2e|SanitizeOperetta32bitsTiffs.groovy ]]** | Removes all 32 bits file from an Operetta dataset - crops values above 65535 | Nicolas Chiaruttini | `#BIOP`, `#Fiji`, `#Operetta` | 2022/03/29 |
| OMERO gists
| --------------
| **[[ https://gist.github.com/4e45b14482a7992fca17d13cf9c94f72|Dataset_Macro-ROIs_Summary.groovy ]]** | [Run Macro on OMERO dataset] This script runs a macro (browsed on the local computer) on all images from an OMERO dataset. It saves the ROIs and the summary (as a csv file and as an OMERO.table) back to OMERO | Claire Stoffel | `#BIOP`, `#OMERO` | 2021/06/02 |