| bf2ometiff.groovy |
Batch conversion to pyramidal ome-tiff using Glencoe Software optimized workflow |
Nicolas Chiaruttini |
#BIOP, #Fiji, #OmeTiff, #MRXS |
2023/06/19 |
| 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 |
| BIOP-userProject.ijm |
A ImageJ macro to create a standardized "User Project" folder. |
Romain Guiet |
#BIOP, #FIJI, #Macro, #UserProject |
2021/06/16 |
| CheckJarsAndUpdateSites.groovy |
Script checking the update sites and some repository |
Nicolas Chiaruttini |
#BIOP, #Fiji |
2022/03/31 |
| checkUpdateSites.groovy |
How to investigate the list of Update Sites enabled |
Nicolas Chiaruttini |
#BIOP, #Fiji, #UpdateSites |
2022/01/14 |
| closeOthers.groovy |
groovy command equivalent to 'close("\others")' in macro language. |
Romain Guiet |
#BIOP, #Groovy, #Macro |
2024/08/09 |
| ComputePSF.groovy |
|
Nicolas Chiaruttini |
#BIOP, #PSF, #Deconvolution |
2024/11/22 |
| CreateLargeImageAndSaveItAsTiff.groovy |
A Fiji script that can generate a procedural big image (>4GPix) and resaves it as a multi resolution OME TIFF image |
Nicolas Chiaruttini |
#BIOP, #Fiji |
2023/01/20 |
| DendritesAnalysis.groovy |
[Spine analysis] Analyse and output cropped images around each spine. Needs a Simple Neurite Tracer input - |
Nicolas Chiaruttini |
#BIOP, #Fiji, #SNT |
2023/09/05 |
| DetectCellsABBA.groovy |
Performs cell detection in QuPath from an ABBA registered project with imported regions |
Nicolas Chiaruttini |
#BIOP, #ABBA, #QuPath |
2024/01/11 |
| 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 |
| 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 |
2023/02/15 |
| ExportCellDataABBA.groovy |
Export Cell Data from an ABBA registered project |
Nicolas Chiaruttini |
#BIOP, #ABBA, #QuPath |
2022/02/08 |
| FijiMultiSeriesExporter.groovy |
Takes a bioformats compatible file and batch exports individual series, optionally Z Projected and rescaled |
Nicolas Chiaruttini |
#BIOP, #Fiji, #BigDataViewer |
2024/11/04 |
| Find_FalsePositive_threshold.ijm |
An ImageJ macro to determine False Positive threshold on control images. |
Romain Guiet |
#BIOP, #FIJI, #Macro, #Coloc |
2024/05/28 |
| GraphLifeTimeVSRepetitionRate.ijm |
A small demo of the Pile-up effect in FLIM imaging |
Nicolas Chiaruttini |
#BIOP, #FIJI, #FLIM |
2023/09/19 |
| 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-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 |
| 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 |
2024/11/15 |
| 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 |
| ImportABBARegions.groovy |
Import Atlas regions in QuPath from an ABBA registered project |
Nicolas Chiaruttini |
#BIOP, #ABBA, #QuPath |
2024/01/11 |
| Lazy_3DAnnotations.ijm |
ij macro prototype for lazy 3D annotations reyling on ROIs interpolation. |
Romain Guiet |
#BIOP, #FIJI, #Annotations, #Labels |
2020/10/29 |
| NikonStereologyBdvVisualizer.groovy |
Takes a Nikon ND2 file and visualizes it lazily in BigDataViewer |
Nicolas Chiaruttini |
#BIOP, #Fiji, #BigDataViewer, #NikonStereology |
2021/03/29 |
| 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 |
| OpenOMERO.groovy |
Open an OMERO dataset into Fiji with caching |
Nicolas Chiaruttini |
#BIOP, #Fiji |
2025/01/24 |
| RecursiFIJI.groovy |
|
Nicolas Chiaruttini |
#BIOP, #BigDataViewer |
2023/05/17 |
| RemoveABBARegions.groovy |
Re-import ABBA regions then filter out regions based on name |
Nicolas Chiaruttini |
#BIOP, #ABBA, #QuPath |
2022/02/10 |
| SanitizeOperetta32bitsTiffs.groovy |
Removes all 32 bits file from an Operetta dataset - crops values above 65535 |
Nicolas Chiaruttini |
#BIOP, #Fiji, #Operetta |
2022/03/29 |