https://www.imagescientist.com/news daily 0.75 2023-06-20 https://www.imagescientist.com/news/qupathqbi-workshop-in-san-diego monthly 0.5 2023-06-20 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/b040bf05-67e2-42a3-9709-e09a7f19ce2e/QBI+LJI+workshop.PNG QuPath News - QuPath+QBI workshop in San Diego - Make it stand out QBI@LJI workshop. https://www.imagescientist.com/news/aqlm-2023-at-woods-hole-ma-usa monthly 0.5 2022-12-21 https://www.imagescientist.com/news/images-to-knowledge-2022 monthly 0.5 2022-05-04 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/23d3653b-5aae-40e8-89ab-202c86bcc56d/I2k.PNG QuPath News - Images to Knowledge 2022 - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.imagescientist.com/news/blog-post-title-one-z3gr4 monthly 0.5 2022-04-15 https://www.imagescientist.com/home daily 1.0 2026-02-01 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622397635750-KYY3V9EFC0MGBU1FLFG3/2021-05-02.jpg Home - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1619465126098-IAQD2DA795RD90CNH6SX/Image+alignment+and+object+transfer.JPG Home - Current Work My research focuses on two main projects: (1) Python-based control software for light sheet microscopy, enabling 3D imaging of collagen networks in cleared tissue, and (2) QuPath-based control software for polychromatic polarization microscopy, designed for integration into clinical pathology workflows. I'm also active in open science initiatives: a steering committee member for QUAREP-LiMi, administrator on the Image.sc forum, and a founding member of BINA's Early Career working group. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1619470325132-1ED6F3COZVR7DQ3D9169/Cytomap+there+and+back+again.png Home - Image Analysis I've worked with QuPath since 2017 and have contributed scripts, tutorials, and workflow guides to help the community get the most out of this open-source platform. Resources here include multiplex analysis workflows, CytoMAP integration for cluster and neighborhood analysis, and scripting tutorials for users at all levels. I also collaborated with Johanna M. Dela Cruz on a video tutorial series for multiplex analysis. https://www.imagescientist.com/current-work daily 0.75 2021-08-23 https://www.imagescientist.com/image-analysis daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1621483830806-2ZCKXFV8H5PM2677BGM9/getting+started.PNG https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1621484243520-OCPGZB7PW9UM0B3INU8V/deeper.PNG https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1621484251553-QPXUL0WR5L9UI0V9AJTY/too+much.PNG https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/b5409aa3-44f8-4a2a-bb1c-f2f0d52854e0/overview+image.PNG https://www.imagescientist.com/microscopy daily 0.75 2026-02-01 https://www.imagescientist.com/about-me daily 0.75 2026-02-01 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1620667569809-3OM63JGTLU00JQEQARPT/Michael_Portrait.jpg About Me - Make it stand out Michael, leaning against a fence above the California coastline. Photo courtesy of Diana Simons. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1624562940998-JHIYKC9ABUAMHGAIQ6XJ/Logo_COBA-Logo.png About Me - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1624563040689-1F8TJIZG600QQZW46CM3/Logo_FIJI-Logo.png About Me - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1624563106888-IHJIBOM1XSYQMRJ90QDJ/Logo_Image-SC-Forum-Logo.png About Me - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1624563152848-UEPQ3GU2Y4JXW75P347J/Logo_Micro-Manager-Logo.png About Me - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.imagescientist.com/qupath-intro daily 0.75 2022-05-16 https://www.imagescientist.com/commenting-in-groovy daily 0.75 2021-07-02 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1621485228869-ASYBRAAY87PQ2T24P3L4/Copying+comments Commenting in Groovy - Line 1 was copied from an unformatted forum post, while line 2 was typed into the scripting window.. 1 will throw an error and fail, 2 works and you can see that the string is correctly formatted (green) https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1621485371825-TS3QV9FSOVVDWWZJN4II/Formatting+forum+posts Commenting in Groovy - The first line was not formatted correctly, and will result in errors if copied into QuPath. The second getPathClass() is formatted correctly, as seen by the background change and colored string on the right. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625234458984-R6MENPK3REJEAVV3BGXA/Creating+a+pop+up+message Commenting in Groovy - Make it stand out A popup is created when no object is selected, as shown. If an object is selected, all child objects of that object are deleted. https://www.imagescientist.com/creating-and-editing-measurements daily 0.75 2023-10-25 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622600542005-YGELQJNGUXVQVWZYO4N7/Two+annotated+tissue+slices Creating and Editing Measurements Two tissue slices, with numbered annotations https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622600576636-3ANAW564EYKGMI96QZVJ/Two+annotated+tissue+slices+with+cells Creating and Editing Measurements Cell detection was run in the initial annotations, and new annotations were added after https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622600900852-JXZO99BCH5HZUUL89LKB/Image+of+Annotation+tab Creating and Editing Measurements Initially, all cells are shown as children of the initial numbered annotations. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622600958163-5WITJRVDV8S76WEK4OWU/Second+image+of+annotation+tab Creating and Editing Measurements After resolving the hierarchy, the cells within the newly drawn Stroma annotations are counted as being below those annotations in the hierarchy https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622602243457-888LI90ZE89H96B1HNPZ/Key+Value+pair+area+showing+new+tissue+slice+measurement Creating and Editing Measurements Key Value pair area showing new tissue slice measurement https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622602233460-X3IU22UOKZP9VWUBBRWY/creating+measurements+5.PNG Creating and Editing Measurements - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.imagescientist.com/loops daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1619545963949-KIIB9ATC84K1BF4LRMIX/Image+of+tumor%2C+outlined+by+software Loops https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1619546098181-8QO5B5QNW8Z1H67OX4OH/QuPath+Menu Loops QuPath tabular menu. The tab “Hierarchy” is selected, with option below for “Tumor (Polygon) (Tumor). A bullet below reads, “Annotation (Rectangle) (6274 Objects) https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1619546235746-5DEMMWF3MRFB6CCFXWDK/Tumor+cells+outlined+by+software Loops A slide with dyed cells. Tumor cells are outlined. https://www.imagescientist.com/strings-and-printing daily 0.75 2021-06-16 https://www.imagescientist.com/selecting-what-you-want daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622490312888-HDPG5UZD2V00IGD1RHZ5/Selection+for+processing Selecting what you want - Make it stand out Since a region was chosen automatically through the dialog, selectAnnotations() will show up in the Workflow tab. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622490427194-AVXHGGA7SO0KPJIO62HQ/selecting+2.png Selecting what you want - Make it stand out The code shows up in the Workflow since the program selected the region to run the cell detection, not the user. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622490776277-3ZBLCEST4FHN7J1TFBTM/A+rectangle+full+of+cells+with+a+manual+annotation+drawn+on+top Selecting what you want - Make it stand out A annotation given the classification “Tumor” was drawn on top of cells generated inside of an unclassified rectangle. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622491892206-RAWW4UTQDYMPIXOOV1PK/Cells+within+tumor+area+are+selected Selecting what you want - Make it stand out Before removeSelectedObjects() https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622491952809-ZLDJL0170WOFMBUW3B63/Cells+within+Tumor+area+are+gone Selecting what you want - Make it stand out After removeSelectedObjects() https://www.imagescientist.com/colorsobjects daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622856081367-489TWHYKRVFUUE262Z4K/The+interface+for+changing+a+class+color Colors-objects - Make it stand out Double click the class you want, select the dropdown for colors, click “Custom Color” and then micromanage the color of the chosen class as much as you want! https://www.imagescientist.com/colorschannels daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622856883888-AR3S0W61WZB0DRU6VDE0/Image+with+long+channel+names Colors-channels - Make it stand out Longer channel names https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622856912785-Z7IYRNHCEOQRHEY4IZI0/Image+with+short+channel+names Colors-channels - Make it stand out Shorter channel names https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622857000007-I995LO2BTJPEEVX3NECH/Chaning+the+first+two+channels+in+the+Luca+image Colors-channels - Make it stand out Displaying only channels 1 and 2 in the LuCa sample image Top: with the default colors, and Bottom: after running the script https://www.imagescientist.com/targeting-objects-additional-methods daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622927529630-ENGL6WNOX0EKUAH4CFWQ/LuCa+image+in+demo+project+showing+results+of+script Targeting objects - additional methods - Make it stand out After running the above script, a group of unclassified cells should have some cells reclassified to “Normal” and recolored white. https://www.imagescientist.com/creating-objects daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1622943751865-A052RNIEUSMBS1I54LHM/Script+results+in+no+measurements+within+tumor Creating objects - Make it stand out As a result of the script removing cells within the tumor area, none of the cells within the tumor area have distance measurements - resulting in the tumor being visible while the stromal cells showing their masks. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623014045620-0Z03BKVMO8DXIR1BW3R9/View+of+Hierarchy+tab+showing+annotations+have+been+duplicated+as+detections Creating objects - Make it stand out The hierarchy shows that the annotations in the LuCa demo project have been duplicated and added as detections. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623015641218-8RRSXG4LK4NMIQ2QVFNF/An+example+of+adding+a+bounding+box+to+an+annotation Creating objects - Make it stand out As advertised, a bounding box is generated around an annotation. https://www.imagescientist.com/editing-object-shapes-or-types daily 0.75 2022-03-31 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623106097355-AJZNVCCJR32FFKIV5I5O/Annotation+removal+before+and+after+script+run Editing objects - Make it stand out A collection of annotations before running the above script (Left) and after(Right). Any annotation that was not at least touching the tissue annotation has been removed. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623107872392-OLKFJCS6DAGI24DBCRGP/Demo+project+results+of+subtraction+script Editing objects - Make it stand out Subtraction of other annotations from the Tissue annotation. The script was run on the demo project after the previous object removal script, so none of the non-tissue overlapping annotations show up. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623108050494-J68EGA9N9ZZR0HEBHCKW/Zoom+in+showing+annotation+expansion+of+a+line Editing objects - Make it stand out Expanding a line annotation (Left and Center) so that the above script will use the expanded annotation to cut the tissue annotation into two pieces (Right). https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623108010240-CLEQBVYQOQ3D34QV78HV/Expanding+a+line+in+order+to+use+it+to+cut+an+annotation+in+half Editing objects - Make it stand out Zoomed out view showing the line cuts all the way through the tissue annotation. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623109228024-8RI4AO5GRILQ8B4OOGOH/Prior+to+running+the+tumor+expansion+script Editing objects - Make it stand out I have added a second Tumor region for fun and testing here - play with the scripts! https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623109278282-8CHNMADR64LUOHPXU8Z5/Demo+project+annotations+after+tumor+expansion+script Editing objects - Make it stand out After running the script, the expansions each show up, labeled and colored. Any tumor area outside of the tissue is clipped off, to make manual annotation easier. Even better, the expansions merge if two tumors are close to each other. https://www.imagescientist.com/creating-a-classifier daily 0.75 2023-10-24 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623111877656-LU9A8HF7TIZUGBHLLBUU/Demonstration+of+using+Brightfield+Other+to+generate+extra+score+compartment+options Creating a classifier - Make it stand out The Image type has been changed to Brightfield (other), and the stain vectors have been renamed to “Hematoxylin1” and “Residual1.” Because of those two steps, a new Positive Cell Detection dialog gives all three channels as options for thresholding. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623112287184-NN3YOQW5JUOMZS7IMIYZ/image14.png Creating a classifier - Make it stand out Example output after using setCellIntensityClassifications() on a set of cells that had already been run through a multiplex classifier. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623112639019-FWRPGC0ZSUWC4BTBD3MD/Class+balancing+when+training+a+classifier Creating a classifier - Make it stand out An example of the Train object classifier interface showing class balancing. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623113381339-9EFRSDXPMVOSPWGEAMG5/Using+the+Cytokeratin+classifier+script+on+the+LuCa+image Creating a classifier - Make it stand out The above script run on the LuCa image in the demo project. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623113490973-XQZA2M9XEA7DMADN0FY4/Adjusting+the+color+of+the+CK+classified+cells Creating a classifier - Make it stand out Now the color has been set to something a bit more similar to the default cytokeratin color in the LuCa image. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623113699380-L31E2Y63GQV9HSB66606/Oops+-+the+colors+are+too+similar Creating a classifier - Make it stand out This may look different when you run the script, as colors are somewhat random. I ended up with two colors that were almost the exact same, but that gave me a chance to go back to the recoloring code. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623113774031-7B8LP1F2PJ885M0Y4PRC/Manually+adjusting+class+colors Creating a classifier - Make it stand out Using the Annotation tab interface to adjust the colors manually. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623113905051-51OPN3YQTM45ZIDVGNTV/Cells+post+color+adjustment Creating a classifier - Make it stand out Now the “CK Small” class cells have been recolored purple, and can be more easily distinguished. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623114197741-LSHW2GIKAX4CGHNGFYRR/A+classifier+decision+tree Creating a classifier - Make it stand out A tentative flow chart for a simple classifier. Hint: the chart is not actually what the code does, can you spot why? https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623114989674-WYEPS8719ALET76P7SWB/An+improved+flow+chart Creating a classifier - Make it stand out Sloppy copy and paste from PowerPoint of the more accurate flow chart. Thanks PPT for reminding me that nonTumor is not spelled correctly. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623115232279-OQLPFGWRZXSUYM0SYPBN/Demonstration+of+classifier+error Creating a classifier - Make it stand out The strongly teal cell in the top center is classified as CK Small, but is very clearly PD1 positive (see channel viewer as a reference for which channel green represents). https://www.imagescientist.com/project-entries-and-functions daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623115983174-QP1MN1K8IWE948IT28LM/image4.png https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623116071498-CF37MZLWUZETSH0UL34T/Results+of+the+pixel+classifier https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623612184398-13EPHORMUYEMZ0C4285I/Output+of+above+script https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623612647975-2QJFPN8ABIA5EYOB53WR/Output+from+script+above https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623612731576-CSIU1KUTQE6UPXA6386Z/Making+sense+of+the+code https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623613267053-F0H56QPGMHFC5MN2YB8T/Output+of+above+code https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623613379634-PKCNWX4XB7LZ7X9NQYG3/Visual+changes+within+QuPath+after+previous+script https://www.imagescientist.com/command-line-and-python daily 0.75 2024-04-24 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623614049778-CGMWG504UEBGX9AKFHL6/Navigating+to+the+appropriate+directory+and+checking+help https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1623617466022-6SLWI9HCCPSMF16091TH/Running+dummy.groovy https://www.imagescientist.com/useful-simple-commands daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/428f28ac-3757-4466-8d36-3a3307bd2599/qupath+outline.png Useful simple commands - Make it stand out An outline of how code objects in QuPath relate to one another. https://www.imagescientist.com/interacting-with-the-file-system-1 daily 0.75 2026-02-13 https://www.imagescientist.com/brightfield-workflow daily 0.75 2021-07-25 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625260711066-MMIU11N69BC4B8PL3FG0/Starting+a+project Brightfield workflow - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.imagescientist.com/brightfield-define-problem daily 0.75 2021-07-22 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625328542941-29YGNL3K7D0577W2T3AV/Regions.PNG Brightfield Define the problem - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.imagescientist.com/brightfield-color-deconvolution daily 0.75 2021-08-08 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625502142200-RFGSWOPZA3240557MG43/Send+selected+region+to+ImageJ Brightfield Color deconvolution - Make it stand out Use the ImageJ button to send the selected region at full resolution (1) to ImageJ with no modifications https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625502457426-JU4FXR657WPU41SG6Z5B/Set+background Brightfield Color deconvolution - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625503155671-A1IOTLYF1Z3LX80RSIKE/visual+stain+editor Brightfield Color deconvolution - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625503255923-8C5BH9ACUCUATGPMF94X/color+inspector+3D+in+Fiji Brightfield Color deconvolution - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625503507291-9HIEMXSW9Y34A3TEUWYI/Red+Blue+view Brightfield Color deconvolution - Make it stand out Fiji’s equivalent of the middle, Red-Blue panel. Blue values go from 0 in the upper right (closest to black) to 255 as pixels reach the “bottom” of the 3D plot. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625504313050-M4IWDBV39V0GRIHQ08BU/visual+stain+editor+after.PNG Brightfield Color deconvolution - Make it stand out Stain vectors after some adjustments. Feel free to use the Exclude checkbox, though I usually prefer to choose to take a little bit of time and annotate areas that are fairly clean. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625504334868-4DG2O3Z5BKW8P1YXHU5K/rename+color+deconvolution.PNG Brightfield Color deconvolution - Make it stand out The renamed color vector sets can be seen in the Workflow tab, and the currently selected one can be found in the Image tab. Another naming scheme might be using the name of the Image where the color deconvolution is performed - so that you can compare between images later. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625504730211-FUTNM3TIGQRN21AAXH4Q/Inspecting+results.PNG Brightfield Color deconvolution - Make it stand out View->Mini viewers->Channel viewer showing the top row. There are 3 main regions of interest to me here. 1. The darker blue tissue shows both hematoxylin and eosin. 2. The fibrotic tissue shows primarily eosin and is almost white in the hematoxylin image. 3. The residual channel (what is left over and not used by the two stain channels) shows some of the highest intensity in the adipocytes, or white space. That is good, because it means there is relatively little error in the tissue itself. I usually find that values of between -0.05 and 0.05 in the residual channel are reasonable, though darker samples (poor scanner illumination) and darker staining tend to lead to higher values. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1625505459286-IM17L1NU7GQJY4LELDT9/teal+and+brown.PNG Brightfield Color deconvolution - Make it stand out Brown staining on the left, and teal staining on the right will show up strongly in the Residual channel. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626204521454-C3KA32YH0GV91N6Q1SA4/stain+vectors+as+script.PNG Brightfield Color deconvolution - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.imagescientist.com/brightfield-3-tissue-detection daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626131787464-U2MDJT55G8IFS99BKE5Z/thresholder+interface Brightfield Tissue detection - Make it stand out The interface https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626131764018-XV2TUIVKAGZO8Z95RXAP/thresholder+menu Brightfield Tissue detection - Make it stand out Where to find the thresholder https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626132656734-DBWA4ERLOGMBQ2JYWKKI/Comparing+choice+of+two+channels Brightfield Tissue detection - Make it stand out On the left, Averaged channels was selected and a Below threshold value of 200 was used to generate the cyan mask. On the right, the Eosin channel was used, and an Above threshold of 0.15 was selected. The results are very similar. If you are ever confused by the values, use the Brightness and Contrast tool to select the channel of interest and use the mouse to inspect pixels for their values in that channel (lower right of the Viewer). https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626133203494-V2BE8W1HXLKJEAHNLT9K/prefilter.PNG Brightfield Tissue detection - Make it stand out While a Gaussian smoothing would increase the total size of the tissue, Morphological closing both maintains a tight border around the edge of the tissue and fills in adipose cells of increasing size as the Smoothing sigma increases. Play around with these settings to see the effects. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626912221088-0ABTL9CAZHY4K68AA5AP/Thresholding+examples.PNG Brightfield Tissue detection - Make it stand out An example of Resolution (R) and Smoothing sigma (S) settings. Top left: R=Extremely low, S = 3. Top center: R=Very low, S=3. Top right: R=Moderate, S=3 Bottom left: R=Very high, S=0. Bottom center: R=Very high, S = 3. Bottom right: R =Very high, S=10. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626134910604-6SMGABSN0PWJG8E87DDW/final+tissue+thresholder Brightfield Tissue detection - Make it stand out I finally settled on this tissue classifier. Moderate pixel size means it will run fairly quickly even on large tissue slices, a little bit of blur helps overcome small gaps in the tissue, and gives me the option of including or excluding adipose cells or vasculature at a later point. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626200404700-UJ6H9TFQYFGE7ZAC9QWR/thresholder+area+selection Brightfield Tissue detection - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626200352766-8ODD0GDX1K9QAUSIY6A9/thresholder+create+objects+interface Brightfield Tissue detection - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626202789561-JIL8D3IYBN7RQFKDMYB2/thresholder+mistake+1.PNG Brightfield Tissue detection - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.imagescientist.com/brightfield-4-pixel-classifier daily 0.75 2023-10-24 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626373421387-2RRWG0AJMAK0OMHJSSZ3/duplicate+images Brightfield Pixel classifier - Make it stand out Using the Project tab to duplicate an image entry, which does not duplicate the image file itself. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626373440924-5O9U49H5OPKS1GI159FW/duplicated+images Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626465873675-CNJSYDDFTIZL6XMXG2P8/classes Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626464975158-DRSSCNKT5NN8R9U1TGLW/Bad+training+data Brightfield Pixel classifier - Make it stand out Bad training data - the majority of it is redundant. Purple with more purple around it. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626465002796-NUG1KOG3XJAABQVSCF2N/At+least+you+tried Brightfield Pixel classifier - Make it stand out Mediocre training data. At least there are a variety of areas sampled, but the center of the tissue is greatly over-represented. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626465028199-HL8YKKLWK832L0NZ1R9J/purple+best.PNG Brightfield Pixel classifier - Make it stand out A more well rounded training data set. This image is zoomed out and more tissue area is covered, but only polylines are used, so the actual amount of training data is much smaller than the other two examples. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626466206444-HS6M72SKL393KWWAPJQ4/Preferences Brightfield Pixel classifier - Make it stand out Return to Move tool automatically has been turned off in Edit->Preferences https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626464344079-TW5OP79CD74O0AP2NK8Y/select+pixel+classifier Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626464323484-Q5VHP6WGVF2DLAD7DYYI/pixel+classifier+menu Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626471522003-AKXO02UF55GZUDC2RONW/variable+importance.PNG Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626558098138-SPHAA9017X94RU194S2E/features.PNG Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626558170395-VU928XC8QK5TEEADPNZQ/features+2.PNG Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626565065383-JQQJCC64BT90SARHI17H/Advanced+options Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626566602847-L3MK4BBD53QRHFWNPL3M/eigenvalue+overlay.PNG Brightfield Pixel classifier - Make it stand out A pair of images showing the Eosin Structural tensor min eigenvalue with a sigma of 4.0, at a Resolution of Moderate. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626566620914-J1IA9KPDCZFXTRJLTVHA/eigenvalue.PNG Brightfield Pixel classifier - Make it stand out Inspecting the overlay with the image in the background shows me that this value is picking up regions of fragmented tissue with lots of edges between Eosin and background. It is also picking up regions within the tissue fold. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626471920923-XHWN332UMNHUD0C5N7R9/check+the+log.PNG Brightfield Pixel classifier - Make it stand out Looking at Variable Importance can let you reduce the complexity of your classifier, making it run faster, and potentially be more generalizable to new data (avoid overfitting). https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626472507055-JM6VEI7K7LCKN98IZ6XD/Mistake.PNG Brightfield Pixel classifier - Make it stand out Orange arrows indicate some of the problem areas. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626473224597-U7WNCPIGVMM01M1CPDZ4/live+prediction+missing.PNG Brightfield Pixel classifier - Make it stand out Where is my pixel classifier overlay?! https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626473474702-ETZQLVT59N3SGEJGMH4P/back+in+business.PNG Brightfield Pixel classifier - Make it stand out Back in business, and the training areas seem to have worked to improve the normal tissue classification. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626473926682-HMWA32I7OZ91D0CCD2GX/createobjects+pixel+classifier.PNG Brightfield Pixel classifier - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626475477773-MMRWXNTUTF627Q3GYIY3/Tile+1+tissue+classifier.jpg Brightfield Pixel classifier - Make it stand out The resulting overlay can be exported manually using File->Export images…->Rendered RGB (with overlays) https://www.imagescientist.com/brightfield-5-cells daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626476343764-M46NC58JOSH1F9T405P9/state+of+the+project.PNG Brightfield Cells - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626478485738-GKCTKDC9Y5F5MA1B0NX7/Test+regions.PNG Brightfield Cells - Make it stand out Several rectangular annotations merged into a single annotation in Tile 4 using Objects->Annotations->Merge selected https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626479212265-YR5TAEQR3NM0THTVLYHN/duplicate+images+3.PNG Brightfield Cells - Make it stand out Current state of the project https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626479464192-45YLA1YDU71YGF4GPE3O/generating+cell+classifier+training+data Brightfield Cells - Make it stand out Adding points to a training area. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626488806769-83FY7R599HVCSQS1YCEY/Object+classifier.PNG Brightfield Cells - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626492495696-3FTZXKHXWICZ05I3LER3/cell+classifier+log.PNG Brightfield Cells - Make it stand out Train object classifier interface and log file from View->Show log https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626492985965-DPM1BD8QEAXI638V531D/select+features+cells.PNG Brightfield Cells - Make it stand out Select features dialog box after unselecting OD and Cell features https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626495257913-EPLBDHQH4NB2O9GK5FIR/results.PNG Brightfield Cells - Make it stand out Results from one image. Due to QuPath using the cell centroid to place a cell “in” a given annotation, some cells at weird edges of annotations will show up as being in the HematoxylinDense areas, despite no cell detection being run there. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626494978933-V6VS7A5GYIS3Q41KWRZ9/Color+view+of+results Brightfield Cells - Make it stand out RGB version of a section of Tile 4 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626495007840-4I9OX55NXSA1BTDF39AT/Optical+density+view+of+results Brightfield Cells - Make it stand out Optical density view of the same section of Tile 4 https://www.imagescientist.com/brightfield-7-finish-and-export daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626495934909-2FI006SBP1XK4LWVMCSW/run+for+project.PNG Brightfield Finish and Export - Make it stand out Note that red text!!!!!!!!!!!!!!!!! Also, do not run the script on images containing training data. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626497027870-H0GANFPAA0C3MLOBSTUI/run+for+project+issue.PNG Brightfield Finish and Export - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626497943154-0IIFB5UNZGYD5OJL6TWU/Export+measurements+dialog Brightfield Finish and Export - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626498741630-OA1GXN3R6N355NLDALQM/results+data.PNG Brightfield Finish and Export - Make it stand out After deleting several columns (or removing them in Columns to include), the results! Areas of various kinds of tissue are generated, along with the percent elongated in EosinDense and NormalTissue. The extra symbol is normal for QuPath exports and can either be fixed or the encoding can be changed in Excel. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626501922200-I9F2NXQ26ESW69DYPODL/prediction+images.PNG Brightfield Finish and Export - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.imagescientist.com/scripting-export-images daily 0.75 2026-02-13 https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626646428366-NEO570OYRPIU2SCHMPFU/export+snapshots.PNG Scripting - Export images - Make it stand out Export Snapshot options: Top Left - Main window content, Top Right - Current viewer content (SVG), Bottom left - Main window screenshot, Bottom right - Current viewer content. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626736644906-MQNWDB7VKWROV8FUNVTN/writeImageRegion.PNG Scripting - Export images - Make it stand out Regions of class Tumor are written out using writeImageRegion https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626736658368-DMJEJSQ3YSHRAO4W45NW/writeRenderedImageRegion.PNG Scripting - Export images - Make it stand out Same regions written out using writeRenderedImageRegion - there are two types of annotations, cyan is classified as Tumor. The unclassified annotations contain cells. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626736677257-E2P6EHHRVSHBDXR3PZPU/writeImageRegion+using+labelServer.PNG Scripting - Export images - Make it stand out writeImageRegion used for Tumor annotations again, but passed a LabeledImageServer with a label set for the cyan annotations and a boundary label set https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626736690847-P559BZDO2BGNBJXQ756P/writeImageRegion+using+labelServer+unique+Labels.PNG Scripting - Export images - Make it stand out writeImageRegion used but passed a LabeledImageServer with useCells() and useUniqueLabels() set. The region used was for the classified annotations, so there is extra whitespace to the side of the cell labels where there are no cells, as seen in the second image. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626829429160-9ENBEPGOFK0U7LEXVRY5/export+examples.PNG Scripting - Export images - Make it stand out Example output from the script above showing the various exports and how the cellLabels images show up as black in Explorer but when opened in Fiji (right) they appear as labeled masks due to the automatic brightness and contrast adjustments. https://images.squarespace-cdn.com/content/v1/60789ef8bebead05cf91ae57/1626643595852-MMSYF55D2WP5G059XDI4/Viewer+options Scripting - Export images - Make it stand out Some of the more useful Viewer manipulation options https://www.imagescientist.com/forum-posts daily 0.75 2021-10-24 https://www.imagescientist.com/mpx-intro daily 0.75 2024-06-19 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