Volumetric Images of *Platynereis* =================================== We demonstrate the results of our pipeline on the marine, annelid worm `Platynereis dumerilii`. We provide two sets of data, which can be downloaded by clicking this url . The directory `01_Insitus` contains data for individual specimens at the developmental stage of 16 `hpf` (or hours post fertilization), which were fixed, stained for the expression of a particular gene and imaged through confocal microscopy. The `DAPI` channel, which localizes the cell nuclei, is made available in the sub-directory `01_Images`. The directory `02_Live` contains several snapshots of one single specimen which was imaged as it developed over time, through Light Sheet Microscopy. The `DAPI` channel is made available for a few time points. .. image:: images/max_insitu_dir2.png :width: 48 % .. image:: images/max_live_314.png :width: 48 % Here above, one can see an exemplary in-situ specimen on the left and an exemplary time frame from the live embryo on the right. The process of chemical fixation leads to shrinking of the embryo, which is why the in-situ specimen appears shrunk, despite being of an equivalent stage. In our project, we address two use-cases: Firstly, **Intramodal registration** where multiple *in-situ* specimens are registered to a reference *in-situ* specimen. For this, we chose to register all *in-situ* specimens to the specimen present in directory `01_insitus/01_Images/04` and called `Pdu_Pax6MHT_16hpf_pNA_PB_20180504-9_dapi.tif`. This implies that 11 images of *in-situ* specimens were registered to one typical, target *in-situ* specimen. Secondly, **Intermodal registration**, where multiple *in-situ* specimens were registered to the corresponding frame from the time-lapse movie which contains an equivalent number of nuclei. This provides us with 7 comparisons. Please note that the sub-directories with the same name correspond to each other, for example, `01_insitus/01_Images/02` corresponds to `02_live/01_Images/02` and so on. Annotated Landmarks ^^^^^^^^^^^^^^^^^^^^ Since for real data the true correspondences are not known, we asked expert biologists to manually identify 12 corresponding landmark nuclei. This set represents ground truth landmarks against which we evaluated the results of our registration based on the average L2 euclidean distance of proposed landmark correspondences. These landmarks, for both the *in-situ* and *live* embryo are available in the sub-directories `*/03_landmarks/`. .. image:: images/F2F0.gif :width: 48 % .. image:: images/F2L0.gif :width: 48 % In the image above, one can see for example, the landmarks labeled 1, ..., 12 in the source (green) image and labeled 1', ..., 12' in the target (magenta) image for intramodal (left) and intermodal (right) use cases, prior to performing any registration.