Microscopy images

The Cell Browser has some basic support for showing microscopy images for your dataset. The basic model is one of sets of images (e.g. stainings for different markers of the same section) arranged into categories (e.g. stages or tissues). Some images can be offered for download only (e.g. TIFFs) and some images can be shown on the screen; these are typically reduced-size versions in JPEG format with sizes of around 1-4k pixels. You provide a JSON file with the description of the images. The Cell Browser then shows an overview of the images on the “Info & Downloads” dialog box.

The default filename is images.json and it has to be placed in the same directory as the desc.conf file. Contact us if you have questions or feedback on this basic system.

In the example below, there is only one image category, called “main category” (there could be several, by duplicating the top-most object and changing the categoryLabel in the copy). This category has two categoryImageSets: the first has the label “DAPI SOX2 TBR2 DCX CTIP2” and offers two files for download and one file for display. The next set has the label “AnotherImageSet” and also has two files for download and one for display:

[
    {
        "categoryLabel": "main category",
        "categoryImageSets": [
            {
                "setLabel": "DAPI SOX2 TBR2 DCX CTIP2",
                "downloads": [
                    {
                        "label": "all merged",
                        "file": "images/cs13-dapi-488-dcx-546-sox2-594-tbr2-647-ctip.tif"
                    },
                    {
                        "label": "DAPI",
                        "file": "images/cs13-DAPI-dcx-sox2-tbr2-ctip2.tif"
                    }
                ],
                "images": [
                    {
                        "label": "all merged",
                        "file": "images/cs13-dapi-488-dcx-546-sox2-594-tbr2-647-ctip.5000.jpg",
                        "thumb": "images/cs13-dapi-488-dcx-546-sox2-594-tbr2-647-ctip.500.jpg"
                    }
                ]
            },
            {
                "setLabel": "AnotherImageSet",
                "downloads": [
                    {
                        "label": "dicom file1",
                        "file": "images/test1.dicom"
                    },
                    {
                        "label": "dicom file2",
                        "file": "images/test2.dicom"
                    }
                ],
                "images": [
                    {
                        "label": "overview",
                        "file": "images/testMerge.jpg",
                        "thumb": "images/testMerge.thumb.jpg"
                    }
                ]
            }
        ]
    }
]

Each image object has a label, a file (the full-size image shown on screen), and a thumb (a small thumbnail). Each download object has a label and a file. All paths are relative to the dataset directory.