├── README.md ├── runCellpose_2D.ijm ├── match_cells_and_nuclei_labelmaps.ijm └── LICENSE /README.md: -------------------------------------------------------------------------------- 1 | # Cellpose-Fiji 2 | ImageJ1 macros to run Cellpose within Fiji (using the BIOP-EPFL plugin) and to match label values in independent labelmaps of nuclei and cell bodies. 3 | 4 | _**NOTE**: These macros will not work with the latest version of the BIOP Cellpose Wrapper! In the comings weeks we will (hopefully find the time to) update this repository._ 5 | 6 | ## runCellpose_2D.ijm 7 | ImageJ1 macro to run Cellpose on an image or active (rectangular) selection and display the segmentation as colored overlay. 8 | Labels are also added to the ROI Manager. 9 | 10 | Input: 2D image or 2D timelapse. 11 | 12 | Output: (timelapse) labelmap, ROIs 13 | 14 | Requirements: 15 | - A working [Cellpose Python environment](https://github.com/MouseLand/cellpose#local-installation). 16 | - Fiji Update Site: PTBIOP 17 | - Follow the [Enable conda command outside conda prompt](https://github.com/BIOP/ijl-utilities-wrappers#-enable-conda-command-outside-conda-prompt-) part of the instructions on https://github.com/BIOP/ijl-utilities-wrappers 18 | 19 | Note that the hard work has been done by others, namely the Cellpose authors and the BIOP at EPFL. 20 | 21 | Please cite the [Cellpose article](https://www.nature.com/articles/s41592-020-01018-x) if you use this macro in a publication. 22 | 23 | N.B. In this macro the 'cyto2' model currently does not work on 2-channel images (cells and nuclei). This should be fixed very soon. 24 | 25 | ![image](https://user-images.githubusercontent.com/33119248/137392416-88a7b8cf-25ee-4116-8b54-b582459e9443.png) 26 | 27 | ## match_cells_and_nuclei_labelmaps.ijm 28 | Macro to match the label values of a nuclei labelmap with a cell body labelmap. 29 | Cells can have multiple nuclei. Nuclei without a cell body are removed. 30 | 31 | Input: Two 2D labelmaps. 32 | 33 | Output: 34 | - labelmap with nuclei labels reassigned to match the cells 35 | - labelmap of the cytoplasm (cell body minus nuclei) 36 | - labelmap of cells without an assigned nucleus (empty cells) 37 | - labelmap of cells without an assigned nucleus minus any other nuclei that overlap, but are assigned to another cell 38 | - (Not yet available) labelmap of nuclei without a cell body 39 | 40 | Requirements: 41 | - Fiji Update sites: CLIJ and CLIJ2 42 | 43 | Please cite the [CLIJ](https://www.nature.com/articles/s41592-019-0650-1) article if you use this macro in a publication. 44 | 45 | Input label images: nuclei and cells (label values do not match - colors are different): 46 | 47 | ![image](https://user-images.githubusercontent.com/33119248/138616840-4ec7daf7-b312-4b33-9da2-3575ce8c05e3.png) 48 | 49 | Output label images: reassigned nuclei, cytoplasm, empty cells with nuclei overlap removed: 50 | 51 | ![image](https://user-images.githubusercontent.com/33119248/138616883-3c390fcc-e729-4942-b3fc-4bc1ed8fbd4c.png) 52 | 53 | -------------------------------------------------------------------------------- /runCellpose_2D.ijm: -------------------------------------------------------------------------------- 1 | /* Macro to run Cellpose on a 2D image or active (rectangular) selection and display the segmentation as colored overlay. 2 | * Labels are also added to the ROI Manager. 3 | * 4 | * Input: 2D image or 2D timelapse image. 5 | * Output: (timelapse) labelmap, ROIs 6 | * 7 | * Requirements: 8 | * - A working Cellpose Python environment. 9 | * - Fiji Update Site: PTBIOP 10 | * - Follow the instructions on https://github.com/BIOP/ijl-utilities-wrappers 11 | * 12 | * Author: Bram van den Broek, The Netherlands Cancer Institute. (b.vd.broek@nki.nl) 13 | * 14 | * Note that the hard work has been done by others, namely the Cellpose authors and the BIOP at EPFL. 15 | * 16 | * Please cite the Cellpose article if you use this macro in a publication: 17 | * https://www.nature.com/articles/s41592-020-01018-x. 18 | */ 19 | 20 | #@ String (label = "Cellpose model", choices={"cyto", "cyto2", "nuclei"}, style="listBox") cellposeModel 21 | #@ Integer(label="Cell diameter", value=20) cellposeDiameter 22 | #@ Float(label="Cell flow error threshold", style="slider", value=1, min=0, max=3, stepSize=0.1) cellposeFlowThreshold 23 | #@ Float(label="Cell probability threshold", style="slider", value=0, min=-6, max=6, stepSize=0.25) cellposeProbability 24 | #@ Integer(label="Cytoplasm channel (-1 means not present)", value=1, min=-1) cytoChannel 25 | #@ Integer(label="Nucleus channel (-1 means not present)", value=-1, min=-1) nucChannel 26 | #@ Boolean(label="Display segmentation as colored overlay on the image?", value=true) displayOverlay 27 | 28 | image = getTitle(); 29 | run("Remove Overlay"); 30 | useSelection = false; 31 | if(selectionType==0) { 32 | useSelection = true; 33 | getSelectionBounds(x, y, width, height); 34 | } 35 | run("Cellpose Advanced", "diameter="+cellposeDiameter+" cellproba_threshold="+cellposeProbability+" flow_threshold="+cellposeFlowThreshold+" model="+cellposeModel+" nuclei_channel="+nucChannel+" cyto_channel="+cytoChannel+" dimensionmode=2D"); 36 | setBatchMode(true); 37 | getMinAndMax(min, max); 38 | if(max < 255) setMinAndMax(0, 255); 39 | print(max + " objects found."); 40 | segmentation = getTitle(); 41 | if(!endsWith(segmentation, "-cellpose")) exit("Cellpose did not return a labelmap"); 42 | rename(segmentation + "__" + cellposeModel + "_diam_" + cellposeDiameter + "_flowTH_" + cellposeFlowThreshold + "_cellProb_" + cellposeProbability); 43 | labelmap = getTitle; 44 | run("glasbey_on_dark"); 45 | resetMinAndMax(); 46 | roiManager("reset"); 47 | setBatchMode(true); 48 | selectWindow(labelmap); 49 | run("Label image to ROIs", "rm=[RoiManager[visible=true]]"); 50 | roiManager("show none"); 51 | setBatchMode(false); 52 | selectWindow(image); 53 | if(displayOverlay == true) { 54 | run("Add Image...", "image="+labelmap+" x=0 y=0 opacity=33 zero"); 55 | if(useSelection == true) { 56 | Overlay.moveSelection(0, x, y); //Move the overlay to the location of the rectangular selection 57 | for (i = 0; i < roiManager("count"); i++) { 58 | roiManager("select", i); 59 | Roi.getBounds(x_roi, y_roi, width_roi, height_roi); 60 | Roi.move(x + x_roi, y + y_roi); 61 | roiManager("Set Color", "gray"); 62 | roiManager("update"); 63 | } 64 | } 65 | } 66 | roiManager("Associate", "true"); 67 | roiManager("Show All without labels"); 68 | if(useSelection == true) makeRectangle(x, y, width, height); 69 | -------------------------------------------------------------------------------- /match_cells_and_nuclei_labelmaps.ijm: -------------------------------------------------------------------------------- 1 | /* Macro to match the label values of a nuclei labelmap with a cell body labelmap. 2 | * Cells can have multiple nuclei. Nuclei without a cell body are removed. 3 | * 4 | * Input: Two 2D labelmaps 5 | * Output: - labelmap with nuclei labels reassigned to match the cells 6 | * - labelmap of the cytoplasm (cell body minus nuclei) 7 | * - labelmap of cells without an assigned nucleus (empty cells) 8 | * - labelmap of cells without an assigned nucleus minus any other nuclei that overlap, but are assigned to another cell 9 | * - (TO DO) labelmap of nuclei without a cell body 10 | * 11 | * Requirements: 12 | * - Fiji Update sites: CLIJ and CLIJ2 13 | * 14 | * Author: Bram van den Broek, The Netherlands Cancer Institute. (b.vd.broek@nki.nl) 15 | * 16 | * Please cite the CLIJ article if you use this macro in a publication: 17 | * https://www.nature.com/articles/s41592-019-0650-1. 18 | */ 19 | 20 | 21 | run("CLIJ2 Macro Extensions", "cl_device="); 22 | Ext.CLIJ2_clear(); 23 | 24 | waitForUser("Select CELL label map and press OK"); 25 | labelmap_cells = getTitle(); 26 | waitForUser("Select NUCLEI label map and press OK"); 27 | labelmap_nuclei = getTitle(); 28 | 29 | Ext.CLIJ2_push(labelmap_cells); 30 | Ext.CLIJ2_push(labelmap_nuclei); 31 | Ext.CLIJ2_getMaximumOfAllPixels(labelmap_cells, nr_cells); 32 | Ext.CLIJ2_getMaximumOfAllPixels(labelmap_nuclei, nr_nuclei); 33 | print("nr of cells: "+nr_cells); 34 | print("nr of nuclei: "+nr_nuclei); 35 | 36 | //Compute the overlap index of each cell with each nucleus. Pair every cell to the nucleus with the largest overlap. 37 | Ext.CLIJ2_generateJaccardIndexMatrix(labelmap_cells, labelmap_nuclei, jaccard_index_matrix); 38 | Ext.CLIJ2_transposeXZ(jaccard_index_matrix, jaccard_index_matrix_transposed); 39 | Ext.CLIJ2_argMaximumZProjection(jaccard_index_matrix_transposed, max_overlap, index_max_overlap); //The index of the maximum is the nucleus with the largest overlap 40 | Ext.CLIJ2_transposeXY(index_max_overlap, index_max_overlap_transposed); 41 | labelmap_reassigned_nuclei = "labelmap_reassigned_nuclei"; 42 | Ext.CLIJ2_replaceIntensities(labelmap_nuclei, index_max_overlap_transposed, labelmap_reassigned_nuclei); 43 | Ext.CLIJ2_pull(labelmap_reassigned_nuclei); 44 | Ext.CLIJ2_release(jaccard_index_matrix_transposed); 45 | Ext.CLIJ2_release(jaccard_index_matrix); 46 | Ext.CLIJ2_release(index_max_overlap); 47 | Ext.CLIJ2_release(max_overlap); 48 | Ext.CLIJ2_release(index_max_overlap_transposed); 49 | 50 | //Find missing values (cells without nuclei) and put them in a labelmap 51 | 52 | //Create binary array of cells without a nucleus (empty cells) 53 | selectWindow(labelmap_reassigned_nuclei); 54 | resetMinAndMax(); 55 | run("Glasbey on dark"); 56 | getRawStatistics(nPixels, mean, min, max, std, histogram); //histogram size is equal to the nucleus with largest label that overlaps with a cell. 57 | 58 | empty_cells = Array.getSequence(nr_cells); 59 | for (i = 0; i < nr_cells; i++) { 60 | if(i<=max) { 61 | if(histogram[i] != 0) empty_cells[i] = 0; 62 | } 63 | } 64 | 65 | //Create cytoplasm labelmap (cell minus reassigned nuclei) 66 | labelmap_cytoplasm = "labelmap_cytoplasm"; 67 | Ext.CLIJ2_subtractImages(labelmap_cells, labelmap_reassigned_nuclei, labelmap_cytoplasm); 68 | Ext.CLIJ2_pull(labelmap_cytoplasm); 69 | changeValues(-1e9, 0, 0); 70 | run("Glasbey on dark"); 71 | setMinAndMax(0, nr_cells); //Set LUT so that the colors match with the other label maps. 72 | 73 | Ext.CLIJ2_pushArray(empty_cells_image, empty_cells, nr_cells, 1, 1); 74 | labelmap_empty_cells = "labelmap_empty_cells"; 75 | Ext.CLIJ2_replaceIntensities(labelmap_cells, empty_cells_image, labelmap_empty_cells); 76 | Ext.CLIJ2_pull(labelmap_empty_cells); 77 | changeValues(-1e9, 0, 0); 78 | run("Glasbey on dark"); 79 | setMinAndMax(0, nr_cells); //Set LUT so that the colors match with the other label maps. 80 | 81 | //Mask part of empty cells that overlap with any nuclei 82 | labelmap_empty_cells_masked = "labelmap_empty_cells_no_nuclei_overlap"; 83 | Ext.CLIJ2_mask(labelmap_reassigned_nuclei, labelmap_empty_cells, masked); 84 | Ext.CLIJ2_binaryIntersection(labelmap_reassigned_nuclei, labelmap_empty_cells, mask); 85 | Ext.CLIJ2_binaryNot(mask, mask_inverted); 86 | Ext.CLIJ2_mask(labelmap_empty_cells, mask_inverted, labelmap_empty_cells_masked); 87 | Ext.CLIJ2_pull(labelmap_empty_cells_masked); 88 | changeValues(-1e9, 0, 0); 89 | run("Glasbey on dark"); 90 | setMinAndMax(0, nr_cells); //Set LUT so that the colors match with the other label maps. 91 | 92 | selectWindow(labelmap_cytoplasm); 93 | selectWindow(labelmap_reassigned_nuclei); 94 | Ext.CLIJ2_clear(); -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | --------------------------------------------------------------------------------